I actually had a similar issue a couple weeks ago. Scenario was my PCs were on a very large ship token (ship had no sight, on object layer so I could easily move it around). PC's had auras from a modified Aura/Tint script (aura 2 only). No matter how I tried to change z-order, PC auras wouldn't show for me (GM) when they were on the ship token, though their token art would. If I moved them off the ship token, I could see their auras again. Not sure if players could see their auras or not; very busy combat so I just rolled with it and moved the ship token to the map layer and navigated it from there, then promptly forgot about the issue until seeing this thread. I'll have to try to repro when I get home and see if it is still happening or if I can glean anything more.