Is the finish on both flanks the same? Is it bad on only one side...which? That can tell you something right there.
On a manual lathe the old school was to set the compound at 29.5deg, with the tool set at the correct angle, so that as you fed in, you were "turning" the flank on the tailstock end and it wasn't rubbing.
Modern controls have the ability to change the way you generate the thread by utilizing different patterns for each tool pass, ....alternating, reducing depth with each subsequent pass, or just straight passes of equal depth.
Assuming you're using good coolant, tool's on center, sharp, rigid part, ...etc...
Try playing with different parameters on some sample pieces...this sounds like a generic and not part-specific problem. My 6061 threads have always come out lovely.