I did some testing with the stock SH4 1.4 seafoam shaders, and I wasn't able to reproduce the blinking problem with them. I agree that the problem seems to be Ati related, but it has so far only occured when using the ROW New Seafoam shaders.
If someone doesn't want to use ROW Classic Seafoam, which seems to fix the blinking problem, then here's a quick and dirty fix. This will bring back the stock seafoam shaders. If you don't have the blinking problem, then you don't need this. If you choose to use this, then please report back if it really works. Enable it with JSGME after TMaru 1.7.1
the fix