I'm with Bucket and Spade, I recently upgraded to 4 gig but I replaced all of the modules. Reading up on the memory it seems if the modules are mismatched in speed then the overall performance drops off significantly.
Are your modules the same PC rating? i.e PC2700, PC5400, PC6400 etc.?
To be honest I thought it was an immediate effect though rather than dependant on amount of usage.
Wasn't there a website PCpitstop or something that would run performance checks on your PC and make recommendations. It may (very remote chance) pick up on this issue.
***Took so long getting this thought out that you've already responded.