I usually use the Fluidmaster ones. The gray part is the included putty. I'm pretty certain your leak is here. You stated the leak stopped for a few weeks, so I would rule out the fill valve for now. There's a good reason why the putty works better.

I had the same thing happen when I finally replaced my flapper with that new kit.

I would bet that where you attached the new flapper kit, with the putty underneath it, you didn't "CLEAN WITH MINERAL SPIRITS AND DRY BEFORE ATTACHING" the new kit. I half-assed cleaned mine the first time and it began leaking again a few weeks later. Took it apart again and followed the directions this time, cleaning and drying it properly, and it's been quiet for 4 years now.