After doing some digging, I somehow succeeded in fixing the problem.
The lost current counters is not only lost in the WMS snap-in it's also not showing in the list of available monitors in the Performance Monitor snap-in.
* I tried to repair the counters with lodctr /r no luck
* I tried to register the counters again with lodctr wmsperf.ini no luck
* I removed the WMS role, added it again with the copied (from another server) config file (ServerNamespace.xml) no luck
* I removed to WMS role, deleted all WMS files, added the role back again (now with the standard config file), WORKS
Now I made a backup of the counters settings with lodctr /s:<filename>, then a stopped the WMS service, replaced the copied config file, run WMSServerConfig /repair, started WMS service (all done as described in http://support.microsoft.com/kb/891773), no luck!
Now I restored the previously saved counter settings with lodctr /r:<filename>, WORKS
So does anyone have any clue what's going on? Bug?!
/Keivan