The change in the way plesk presents the logs can cause some frustration. The 'access' comments just signify that the entries are from one of the access logs. All site trafic, normal or otherwise gets logged in the access logs.
There is nothing wrong with these entries. Point to note most of the 'errors' I see are just the lack of a 'robots.txt' file on the domain.
I'd definitely repremand your colleague over disabling the firewall. If one person can't access the ftp whilst others can then there's no problem with the server - unless their IP or client has been blacklisted/blocked.
Post #2 I can't reply 100% with my lack of experience with that error - other than to say it looks like something was enabled (an Apache module) without a setting, and was disabled by your server. Hence the 'warning' and not 'error'.