That sounds similar to some things I experience. However, the shifting problems I ran into have two sources: One is the infamous skip shift/CAGs that blocks you out from shifting from 1st into 2nd or 3rd (it wants you to go to 4th) under moderate acceleration. The other though thing I run into, that isn't so annoying, is the shifter is just real..mechanical feeling, in a somewhat old fashioned way. Like, sometimes I will feel more resistance putting the shifter into the same gear, under the same conditions, compared with another time. Also, on occasions, I will move the shifter into a gear and the shifter doesn't go as physically far into that gear. However, if I re-clutch, remove the shifter stick, and re-put it back into the same gear it will go further. Sorry for my non-technical attempt at description, but I'm not very mechanically inclined.
BTW, my car is fully stock, I've driven sticks before, and I always push the clutch all the way to the floor before attempting to shift.
06 IBM/blue M6 18"