This is still an issue in winamp 5.63:
I think the bug is with the 'Automatically add played files' option,
which is under preferences-local media then the watch Folders tab.
Having the 'Automatically add played files' checkbox unselected obviously should mean new tracks do not get added to the library, but if they are already there, it seems reasonable that their play counts are increased, and the track added to the recently played list.
However if that option is not selected, and you play a track directly from your file manager or from a playlist within winamp, (despite the track already being in the library),
you can get different results:
If the track has never been played before, it will not be added to the recently played list or have its playcount increased to 1.
If it has been recorded as having been played before, then the counts are increased as expected.
Play the same track directly from the library, then the counts are increased as expected.
I think winamp mistakenly looks for the track in the played tracks lists rather than all audio tracks, to determine if the track is new to winamp.
So I suggest the immediate work around for problem like this, is make sure the 'Automatically add played files' checkbox is ticked.
(I've only started taking an interest in playcounts now you can successfully back them up and edit them, albeit through the export/import xml functionality.)
Keep up the good work winamp teamers - it is still a great product.