All mine have locations defined, yet since sometime last week I started suffering from the giganto PVP icon problem.
Which is weird considering I haven't seen the problem for months and haven't changed anything.
I recently reset my PitBull config for my character profile and started from scratch, with focus on icon placement. I removed the modules I didn't use and ensured that all icons had a placement defined.
I still encountered the icon sizing/distortion issue, while in PvP battlegrounds only. Seems to take place most often if I view the map, then return to normal gameplay view. I have had zero issues in PvE play.