Ed,
I'd try slowing lightening the chipload - or bite that each flute takes per revolution of the spindle/router. You can do this a few ways...
1) Increase RPM
2) Reduce Move Speed
3) Use a 2 or 3-flute spiral-O (Onsrud 65-624 or similar)
You should put your safety glasses on (with side shields!) and get in there and observe what is going on as the parts are being cut. Are they lifting? If so, and you have reduced chipload without melting, it could be that you either don't have enough vacuum pressure or that the helical flutes of the tool are working against you - causing lifting. ANY vibration from parts lifting even a little bit, will degrade the cut quality. Parts should NOT be moving if you are using the technique & materials I outlined above. Substitutions for other products or methods will give varying results.
If the spiral tools are lifting parts & you've done all you can do, try a 2-flute straight-O tool, which will leave chips in the kerf, aid hold down and still give a decent cut. I would not advise using straight flutes on plastic over 1/4" though, because you really want to get those chips out of there.
Reduction in cut quality is in most cases, directly associated with worn pinions and dry gear racks...You'll also want to check the machine under power, not moving, by grabbing every axis and push/pull - listen and feel for slop in each axis. Really shake everything and listen for the tell tale 'ticking' of slop. I am not talking about the slight ticking that you hear from a 7.2:1 gearbox - this is normal. Check the v-rollers...Clean each and every rail with a scotch pad - every little bump in the rail will transfer to your cuts.
You should be running those small bits between .5 & 1 IPS and 18,000 RPM. If you are not, your chipload is probably too high.
-B