Man, that has got to be frustrating. I have never had a problem like that but don't use water based dyes.
I get really good results with the following method:
1) cut the resolene 50/50 with water
2) wet a sponge (I normally use something about 3" x 3") and squeeze the water out of it so that the sponge is just damp)
3) wrap the sponge with a soft cotton cloth
4) dip the cloth wrapped sponge into the diluted resolene and squeeze it out so that the cloth is just damp
5) wipe the item with a continual stroke, in one direction, very, very, lightly
6) wait for an hour or so, until it is dry and then repeat
I find that three coats like this is sufficient to seal the dye and yet it does not alter the feel of the leather
Once I have coated the leather to my satisfaction, I let it sit at least overnight before I flex or work with it.