Are you referring to the tailBeacon, or the tailBeaconX?
I found that the tailBeaconX was a little too long for the tapered fairing for the tail-light on my 1996-era RV-6. uAvionix includes a spacer that lets you mount it 1/4" further aft in the hole, which solves this.
An RV-7 owner I know also found this problem, and elected to re-fibreglass the taper to increase the clearance. The tailBeaconX sits more flush and looks better done this way. I may upgrade mine as well.
1996 RV-6 "Tweety" C-FRBP (formerly N196RV)