Need help with clear flats

Sounds like something is wrong here. Why does the clear flat appear "almost coarse or kinda chalky?" How long are you letting the Tamiya acrylic dry before spraying the MM flat?

It almost sounds like (a) you're applying your flat coat too heavily, and (b) the flat coat may not be thoroughly mixed. Are you using MM flat in a spray can or airbrushing it?

Try applying your flat coat using light mist coats and letting each coat dry between coats to avoid it affecting the paint and decals below. This will also help you to achieve the level of "flatness" you require.

I use Gunze (acrylic) clear flat (H-20) and apply in light coats as described above.

I switched over to Polly Scale clear flat a year or two ago, and have had great results with it. 

Hmmmmmm, I use MM Clear Flat too and haven't had any problems, even though I generally brush paint it on, but - it's almost always going down over MM enamels, so you have an enamel going on top of an enamel, which greatly reduces your chances of one of the 9 bazillion acrylic/enamel reactions we all live in fear of.

If you don't want to use Future as a barrier coat between the Tamiya acrylics and the MM Flat, and you use an airbrush, then look into the Tamiya Flatener (X-20? I think). Just remember that it is an additive, and has to be mixed with one of the Tamiya clear coats to give you a flat finish.

I brush paint the flat on. And I would usually not do that for a while after the project dried. I would let a model sit for sometimes a month before remembering to put a flat coat. Is there something special about putting a gloss on before the flat coat? Other than for decaling, which I put on flat paint and work great still.