Bukkit

What Version of OnTime and Bukkit are you using?
OnTime: 4.1.0
Spigot: 1.8

What storage option are you using? (YML or MYSQL) ?
MySQL

What permissions plugin are you using? (Groupmanager, PEX,bPermissions, etc.)
PEX

Please provide a link to a copy of your plugins/OnTime/config.yml:
http://pastebin.com/qvBJtFbX

Did you turn on OnTime logging (/ontime logfile enable 1)?  If so, provide a link to that file too.
Ontime error log (goes quite far back): https://www.saladcraft.net/files/OnTime_ERROR.zip

Please provide any additional information below.

Some player records who had their playtime manually changed after a username update prior to V4 are working fine, others have reset. Players who changed names after v4 are not getting the same playtime on every server, and for some records it shows the player as offline when they switch to a different server (checked from the server they are on).

Setting 'multiServer' to true and using 'mulitServerName' does not fix the situation, neither does filling it 'serverName' with unique names for each server. This is why i have them disabled in pasted config.

I can provide a copy of the ontime-players table if needed.

I am going to tackle the multi player record issue (single server systems) issue first, which also applies to the issues you are seeing, and I will tackle the larger issue of fixing the multi-server configurations.

Thanks for supplying all the extra info for the ticket. It helps very much! (Please see PM for additional request.)