Assets not appearing on upload

I've resolved the upload issue (that was a local conectivity problem) however the missing files is more worrying. I'm in the process of reuploading them all.

    Perch: 2.8.15
    Production mode: Production (100)
    Installed apps: content (2.8.15), assets (2.8.15), categories (2.8.15), perch_forms (1.8.3), perch_gallery (2.8.6), perch_mailchimp (2.0.1), perch_blog (5.0), perch_newsfeed (1), perch_comments (1.1), perch_members (1.4), perch_backup (1.2), perch_twitter (3.5.1)
    DB driver: PDO
    DB tables: perch2_blog_authors, perch2_blog_comments, perch2_blog_index, perch2_blog_posts, perch2_blog_posts_to_tags, perch2_blog_sections, perch2_blog_tags, perch2_blogs, perch2_categories, perch2_category_counts, perch2_category_sets, perch2_content_index, perch2_content_items, perch2_content_regions, perch2_forms, perch2_forms_responses, perch2_mailchimp_campaigns, perch2_mailchimp_history, perch2_mailchimp_log, perch2_mailchimp_stats, perch2_mailchimp_subscribers, perch2_members, perch2_members_forms, perch2_members_member_tags, perch2_members_sessions, perch2_members_tags, perch2_navigation, perch2_navigation_pages, perch2_newsfeed, perch2_page_templates, perch2_pages, perch2_resource_log, perch2_resource_tags, perch2_resources, perch2_resources_to_tags, perch2_scheduled_tasks, perch2_settings, perch2_twitter_scheduled_tweets, perch2_twitter_settings, perch2_twitter_tweets, perch2_user_privileges, perch2_user_role_privileges, perch2_user_roles, perch2_users
    Users: 2
    App runtimes:

    <?php
        $apps_list = array(
            'content', 
            'categories',
            'perch_blog',
            'perch_comments',
            'perch_forms',
            'perch_mailchimp',
            'perch_members',
            'perch_twitter',
            'perch_newsfeed',
        );

    Scheduled tasks for perch_blog: delete_spam_comments (1440 mins)
    Scheduled tasks for perch_mailchimp: update_list_stats (60 mins)
    Scheduled tasks for perch_twitter: post_tweets (1 mins), update_tweets (10 mins)
    Scheduled tasks for perch_newsfeed: update_news (1440 mins)
    Editor plug-ins: ckeditor, tinymce, redactor, markitup
    H1: 79a8ac065165c0a0be89b727cbba9fd0
    L1: e1c252c3a4472f148eba51660f761193
    headerColour: #ffffff
    content_singlePageEdit: 1
    helpURL:
    perch_mailchimp_secret: 60e4accf6814078a980df398cd18fded
    hideBranding: 1
    content_collapseList: 1
    lang: en-gb-alt
    update_2.8.8: done
    latest_version: 2.8.15
    on_sale_version: 2.8.15
    headerScheme: light
    dashboard: 1
    hide_pwd_reset: 0
    content_hideNonEditableRegions: 1
    content_frontend_edit: 0
    perch_blog_update: 5.0.1
    perch_blog_post_url: /news/post.php?s={postSlug}
    perch_backup_mysqldump_path:
    perch_blog_slug_format: %Y-%m-%d-{postTitle}
    perch_blog_akismet_key:
    perch_blog_max_spam_days: 1
    perch_comments_akismet_key:
    perch_gallery_bucket_mode: dynamic
    perch_gallery_bucket: default
    perch_mailchimp_api_key: d14886cc8f69d57462b8d13ccb0572d6-us4
    perch_mailchimp_list_id: a5132b78a9
    perch_mailchimp_campaign_url: /mailchimp/campaign.php?s={campaignSlug}
    perch_members_login_page: /members/login.php?r={returnURL}
    perch_blog_comment_notify: 1
    perch_gallery_basicUpload: 0
    siteURL: /
    perch_mailchimp_update: 2.0
    logoPath: /admin/resources/logo-RW.svg
    update_2.8.10: done
    perch_twitter_update: 3.5
    update_2.8.11: done
    update_2.8.13: done
    update_2.8.14: done
    update_2.8.15: done
    perch_members_update: 1.4
    PERCH_DEVELOPMENT: 10
    PERCH_STAGING: 50
    PERCH_PRODUCTION: 100
    PERCH_DB_USERNAME: cl18-rapture
    PERCH_DB_SERVER: localhost
    PERCH_DB_DATABASE: cl18-rapture
    PERCH_DB_PREFIX: perch2_
    PERCH_TZ: UTC
    PERCH_EMAIL_FROM: rebecca@raptureandwright.co.uk
    PERCH_EMAIL_FROM_NAME: Rebecca Aird
    PERCH_LOGINPATH: /admin
    PERCH_PATH: /home/sites/raptureandwright.co.uk/public_html/admin
    PERCH_CORE: /home/sites/raptureandwright.co.uk/public_html/admin/core
    PERCH_RESFILEPATH: /home/sites/raptureandwright.co.uk/public_html/admin/resources
    PERCH_RESPATH: /admin/resources
    PERCH_HTML5: 1
    PERCH_SCHEDULE_SECRET: junkanoo
    PERCH_RUNWAY:
    PERCH_ERROR_MODE: DIE
    PERCH_DATE_LONG: %d %B %Y
    PERCH_DATE_SHORT: %d %b %Y
    PERCH_TIME_SHORT: %H:%M
    PERCH_TIME_LONG: %H:%M:%S
    PERCH_DEBUG:
    PERCH_PREVIEW_ARG: preview
    PERCH_TEMPLATE_PATH: /home/sites/raptureandwright.co.uk/public_html/admin/templates
    PERCH_DEFAULT_DOC: index.php
    PERCH_DEFAULT_EXT: .php
    PERCH_PRODUCTION_MODE: 100
    PERCH_RWD:
    PERCH_HTML_ENTITIES:
    PERCH_SSL:
    PERCH_STRIPSLASHES:
    PERCH_PROGRESSIVE_FLUSH: 1
    PERCH_AUTH_PLUGIN:
    PERCH_DB_CHARSET: utf8
    PERCH_DB_PORT:
    PERCH_DB_SOCKET:
    PERCH_SESSION_TIMEOUT_MINS: 20
    PERCH_APPS_EDITOR_PLUGIN: markitup
    PERCH_APPS_EDITOR_MARKUP_LANGUAGE: textile

Hosting settings

    PHP: 5.5.30
    Zend: 2.5.0
    OS: Linux
    SAPI: cgi-fcgi
    Safe mode: not detected
    MySQL client: mysqlnd 5.0.11-dev - 20120503 - $Id: 15d5c781cfcad91193dceae1d2cdd127674ddb3e $
    MySQL server: 5.5.35
    Extensions: Core, date, ereg, libxml, openssl, pcre, zlib, bz2, calendar, ctype, hash, filter, ftp, gettext, gmp, SPL, iconv, pcntl, readline, Reflection, session, standard, shmop, SimpleXML, sockets, mbstring, tokenizer, xml, cgi-fcgi, bcmath, curl, dom, enchant, fileinfo, gd, imap, intl, json, ldap, exif, mcrypt, mssql, mysqlnd, mysql, mysqli, odbc, PDO, pdo_dblib, pdo_mysql, PDO_ODBC, pdo_pgsql, pdo_sqlite, pgsql, Phar, posix, pspell, recode, soap, sqlite3, sysvmsg, sysvsem, sysvshm, tidy, wddx, xmlreader, xmlrpc, xmlwriter, xsl, zip, mhash, ionCube Loader, Zend Guard Loader
    GD: Yes
    ImageMagick: No
    PHP max upload size: 64M
    PHP max form post size: 64M
    PHP memory limit: 128M
    Total max uploadable file size: 64M
    Resource folder writeable: Yes
    Session timeout: 24 minutes
    Native JSON: Yes
    Filter functions: Yes
    Transliteration functions: Yes
    PATH: /usr/local/bin:/usr/bin:/bin
    UNIQUE_ID: VkRGGX8AAAEAAEqvZ7QAAAAX
    SCRIPT_URL: /admin/core/settings/diagnostics/
    SCRIPT_URI: https://raptureandwright.co.uk/admin/core/settings/diagnostics/
    HTTP_HOST: raptureandwright.co.uk
    HTTP_USER_AGENT: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:44.0) Gecko/20100101 Firefox/44.0
    HTTP_ACCEPT: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
    HTTP_ACCEPT_LANGUAGE: en-GB,en;q=0.5
    HTTP_ACCEPT_ENCODING: gzip, deflate
    HTTP_REFERER: https://raptureandwright.co.uk/admin/core/settings/diagnostics/
    HTTP_COOKIE: __atuvc=53%7C45; _ga=GA1.3.1475504153.1447259288; cmsa=1; cmssb=0; PHPSESSID=5nh02mgdr3mlq01828mh2fua43; p_m=3bc50efdcb5906a019d5a71f0cc9209e69cb260a; __atuvs=56444027669e5208011; _gat=1
    HTTP_CONNECTION: close
    SERVER_SOFTWARE: Apache/2.4.10 (Unix)
    SERVER_NAME: raptureandwright.co.uk
    SERVER_ADDR: 10.0.1.178
    SERVER_PORT: 80
    REMOTE_ADDR: 92.31.70.246
    DOCUMENT_ROOT: /home/sites/raptureandwright.co.uk/public_html
    REQUEST_SCHEME: http
    CONTEXT_DOCUMENT_ROOT: /home/sites/raptureandwright.co.uk/public_html
    SERVER_ADMIN: root@localhost
    SCRIPT_FILENAME: /home/sites/raptureandwright.co.uk/public_html/admin/core/settings/diagnostics/index.php
    REMOTE_PORT: 39707
    GATEWAY_INTERFACE: CGI/1.1
    SERVER_PROTOCOL: HTTP/1.1
    REQUEST_METHOD: GET
    QUERY_STRING: extended
    REQUEST_URI: /admin/core/settings/diagnostics/?extended
    SCRIPT_NAME: /admin/core/settings/diagnostics/index.php
    PHP_SELF: /admin/core/settings/diagnostics/index.php
    REQUEST_TIME_FLOAT: 1447314969.5017
    REQUEST_TIME: 1447314969

Will do.