I just thought I'd share this problem (bug?) I found on Trapcode Form and a workaround I found as I'd hate anyone to tear as much hair out over it as I did.
Basically I had the Trapcode Form effect on a Shape Layer. I was using a pre-composition as a Custom Particle. For some reason this caused the particles to blink on and off (almost rhythmically).
I spent ages trying to work out what it could be and then I discovered that if I made sure the visibility of the pre-composition layer was turned on then it fixed it. Obviously I've just had to turn the transparency to 0% instead.
Anyway, like I said, I thought I would just share,