Any of the server owners can contact me via xfire: "akkthedude", about this problem. I was a server owner of a pretty active jaymod server for about 2 years. I dont believe it's just a jaymod issue, if I can see the server.cfg file I think I got a chance to tell you whats wrong in there...
I do believe there's something wrong with the config atm. Any changes made there latetely? A standard jaymod cfg issue is that it's important where the exec user.db or level.db is written in the config. First add the g_schrubbot line and the level.db and exec user.db and all this, then afterwards add the xp_save line. If the XP-save lines are written before the execing of the schrubbot, xp can be lost in jaymod, dont know why, but thats my expierence. PB can be the problem too, or something wrong with the execing of user.db file, or even a full user.db file can cause this (jaymod user.db file can only store up till about 7000 player ID's, so XP-save for ever is impossible on very active servers).
If the problem cant be fixed, I suggest you switch to another jaymod version, like 2.1.10 instead of 2.2.0, cause even I agree XP aint important, you'll loose players this way. Afterall not only XP is lost, all levels are gone too (this means the user is deleted, or not recognised via the user.db file or via PB). And guys, one other thing: stop uploading maps without waypoints for bots. If you need waypoints for a map, but you cant find any on the internet, ask me, I'll make them in 10min.
Thanks for help The Dude!
It's not config issue because if it would be then after mass prune, it shouldn't save XP either. In jaymod, you don't need "exec" or add "exec" in config for loading db files because on each map load it auto read those files from mod folder, saves in memory and auto writes on each map end. g_shrubbot doesn't exist in jaymod 2.1.7+
PB can't be problem because we don't have PB and even when we had PB we had same issue.
Jaymod 2.1.7 user.db can store up to 9999 user ID and Jaybird extended it in 2.2.0 on my request but it seems it doesn't work correctly once you go above that limit. More or less we don't have XP save forever. It's for 30 days and after that it gets deleted unless user has admin level.
Going back to 2.1.10 will change nothing because it's somewhere core code issue. Can you please tell me which maps on server are missing wavepoints? Please report it on tracker and if needed we will contact you for waypoints.
Thanks for offering help but you are little off the track with jaymod settings.