Are you playing flash games embedded into web pages or downloading the .swf and playing them stand-alone in their own browser tab?
Many flash games run much better without embedding.
EDIT: One recent example: I played GemCraft for a while last week. Embedded in ArmorGames' website in either IE or FF, the game was getting increasingly laggy minute by minute until it crashed after 15-20 minutes of use every time I loaded it. After saving the .swf and loading it directly in a blank page, it was running perfectly fine for hours.