So, the problem is occurring in PCB at the moment. I'm using the Vsync patch to counteract the control input lag issue, of course. Anyway, I've tried forcing wait for vertical refresh/triple buffering on the graphics card (ATI Radeon HD 4600 series), using Riva Tuner's D3DOverrider to force Vsync/triple buffering, I even thought that it was a ground loop issue at one point! Also, at one point in the past, I also noticed screen tearing with Winamp's Visualiser, but with triple buffering enabled, this problem seems to have disappeared. Strange how it shouldn't work with Touhou...
If anybody has managed to fix the same sort of problem before, I'd be very pleased to hear from you.