A short preface: I used Gsnerf's gentoo ebuild to install Plex Media Server, and it's sadly a bit outdated but I doubt this is the problem here.
After trying Plex on my main workstation, I was convinced it was the optimal media solution for my home network, so I set about installing it on my gentoo-based gateway/all around server. I've managed to set it up succesfully, but I'm finding that scanning files is a lot slower than it was on my workstation. Both server and workstation are similarly specced, however: an i7-875K on the workstation, an i5-3470 on the server. Both have 8GB RAM, and the only significant difference (other than the obvious OS difference) is that the PMS database resides on a SSD on the workstation and on a HDD on the server.
The real issue seems to be something in the way it accesses the database, because Plex Media Scanner.log is riddled with these warnings, especially when scanning music:
Aug 04, 2013 06:46:26 [0x3c56801c740] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:26 [0x3c55bfce700] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:28 [0x3c56801c740] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:30 [0x3c55bfce700] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:31 [0x3c560a2a700] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:32 [0x3c55bfce700] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:33 [0x3c56801c740] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:35 [0x3c56801c740] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:35 [0x3c560a2a700] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:36 [0x3c55bfce700] WARN - Waited one whole second for a busy database. Aug 04, 2013 06:46:37 [0x3c56801c740] WARN - Waited one whole second for a busy database.