Interestingly, when I grain filled my ash strat body I thought I had it dead smooth. That was until I started with the dye. I'm pretty sure that the water in the dye re-hydrates the Timbermate and I was basically pulling it all back out of the grain again (since the grain valleys are so wide) with each wipe of the dye cloth. This may be your issue given how many coats of colour you have added. Personally I had to end up filling the remaining undulations with clear coat to get a uniform final finish.

cheers,
Gav.