Are you in a part of the instance where a boss should show on the map? Note that some instances (like all the classic raids, BC and Wrath dungeons, etc.) don't support boss markers anyway because they don't have Dungeon Journal entries.
UseQuestLogSpecialItem has been protected since its introduction; that's nothing new. There are just a lot of things you can't do without tainting the objective tracker, period. Your options are really (a) don't use any addons that touch the tracker or the world map or any of a dozen other things, or (b) use another addon to replace Blizzard's badly coded buttons with ones that aren't broken by looking at them sideways, or (c) use some other method of using quest items.
FWIW, I use Mapster at all times and the buttons work fine for me.
There is one known limitation, that is if you use the map size toggle in the title bar of the map window, it'll break the button. Unfortunately, due to the way the map and the quest things are integrated, this is rather hard to avoid.