I'm sure you have decided not to use Undef's Record Eyepiece
for a good reason, if not I strongly recommend trying that plugin, see if it helps on the overlap.
With that many people on the server you are bound to get some lag with the manialinks. Out of curiosity, what is your server running on? It appears there is a memory leak on most *nix based systems, see here
for more info. Over time the memory leak will have a knock on effect for the PHP/Manialink stuff resulting in overlapping on map changes.
Not really any fix there for your problem, sorry.