@FullTankHave you tried removing the mods that have a direct affect on the gun markers? Start by removing Gun Marker #7 and the Over Target Markers. Others have reported problems with the mods that use hud_lib.swf so I would also remove all of those. Aslain told me he will either work with the authors to fix Sixth Sense and Trap Sense or try to work on them himself as both of those popular mods are causing problems.
Also, take a look around the forums. Others are having the same problems. You could see if any of the advice that helped them will help you as well.