We were unsure if GISD would be entirely "animation stable" but the good news is that it appears to be so, at least in all the tests I've done. So I don't think GISD is responsible for your problems.
GISD *does*, to my recollection, affect the GI cache as well, though that's only part of the effect. In general I'd recommend keeping it on until and unless you're sure it's causing issues.
Martin's suggestion is more along the lines of what I think will resolve the problem. I'm not sure where you read that the more GI cache frames you have the better - it's actually *somewhat* the opposite. The fewer frames you're blending, the smoother the result will generally be (within reason) because there's less variance between them. But you want to strike a balance between e.g. using just a single cache file for an entire animation (static GI, essentially, even if lighting changes) and using 1 for every frame (every frame's lighting changes are represented in GI, but it can create flickering).
So basically the recommendation is, as Martin said, to render every 4th or 5th frame or so, then blend between 3 and 5 frames. I would suggest starting by rendering a GI cache for every 5th frame. Then set it to Interpolate for Animation and blend 3 frames. If there is still flickering, try blending 5 frames. Note that the more frames you are blending, the bigger the render time and memory impact.
- Oshyan