Latest update
The latest update (the one with the new trophies/achievements in preparation for the DLC) seems to cause weird glitches with the mini-map.
The problem seems to be that if you turn off certain icons on the map, different icons disappear from the map too. I downloaded the update this morning, then started messing around with some Templar missions while waiting for the DLC. I turned off everything except tunnels and Templar mission indicators, but after marking the nearest mission start marker, it never showed up on the mini-map. The distance to it was still correct, though.
Also, I turned off the landmark markers, and they still showed up on the map (and mini-map).
I'm sure it will have other annoying effects, until Ubisoft issues another patch to fix it (I hope).
Forewarned is forearmed! (Although, who is 4-armed anyway?)
EDIT: Forgot to mention that this is the PS3 version. I don't know if it affects the Xbox or not.