I had a similar problem with my old computer. Usually it would drop to around 40fps partway into a stage, and then sit there until the stage ended. Never did figure out the cause or a fix, but I assumed it had something to do with the way the game handles objects, since it happened a lot faster on higher difficulties where there's more bullets and stuff. Vsync helped a little and made Easy/Normal mode playable, but it didn't really fix anything so much as make it not as bad. Could maybe try 1/2 frameskip or something too, but it makes things a little harder and it's tough on the eyes.