I am no expert on the subject, but I have had a similar issue ongoing with Tamiya Acrylic, I am hoping I will get better results when I get my hands on their new retarder - as someone said above, although not always necessary I think that using same brand everything is wise.
Do you prime your models?
Although some suggest it isn't really required, I usually prime before painting, this assists in smoothing out fine flaws, gives the colour coat something even to go onto & promotes adhesion - it is just the mindset I have always had - prime, then paint.
However, looking through my built kit's from the last couple of years, one thing stands out like a sore thumb, the two kits which I did not prime way & by far have the better finish in terms of texture. Now I know the obvious conclusion here is that the primer coat on the primed kits was rough to start with, but that was not case, all the primed kits have been done with Mr Surfacer 1200, which was checked for smoothness & sanded / polished as required, leaving a finer / smoother finish than any Tamiya Acrylic has done for me.
This has left me wondering if there is something going on when the colour coat hits the primer, not a typical style paint reaction that you would get regular incompatibility or inadequate drying, but some other sort or reaction between primer & top coat that is preventing a smooth "lay down"?
Triarius - being our resident expert, could you comment on the possibility of this?