Observed this problem on Precise with Unity 5.x already - now on Quantal with Unity trunk the Launcher behaves the same way.
I already reported this problem, but it might be configuration and multi-monitor specific - so it seems hard to reproduce.
Please see the attached video, it also shows CCSM Ubuntu Unity Plugin and Displays settings.
Note:
1. Once the mouse is moved to hover over an icon, I can stop the launcher from autohiding (see video).
Conclusion: Icon hovering detection is working. More testing shows that this is true for all of the Launchers on all monitors.
2. I can move the pointer on top of the revealed Launcher - it will still autohide (see video).
Conclusion: No matter if moving the pointer over the revealed launcher, it does not detect it. This bug just affects one of the 3 Launchers.
3. Note that the bug even occurs, if all Launcher settings are set to defaults, except for autohiding being enabled, no matter if set to show on "Primary" or "All Displays".
Conclusion: Some broken or experimental settings are not causing the problem.
4. While in System-settings->Displays you can set "Launcher Placement" correctly for 3 displays, can choose which one you want the Launcher to be on and this setting also is applied and works, the Ubuntu Unity Plugin does not reflect this and you can just choose between "Primary Display" or "All Displays" there, whatever "Primary Display" will reflect then.
Conclusion: Needs investigation, probably just a change from "Primary Display"->"One Display" is needed.
5. If I set the Launcher to autohide, but to show on all Displays in my triple monitor configuration, it will not have the bug on monitor 2, nor monitor 3, just on the monitor I originally wanted the launcher to be on (monitor 1).
Conclusion: In a 3 display configuration, 2 Launchers work perfectly, just one shows broken hovering detection.
6. It is hard to work with the Launcher if it behaves that way. ;)
Conclusion: Need to rearrange my monitors physically or fix that nasty bug.
7. So it seems that probably I could fix this problem by manually re-arranging my monitors in the real world, so that monitor 2 or monitor 3 would be the outermost left ones and show the Launcher just there, but I would not want to do that work and would rather like to see this fixed in the code ;)
8. More investigation shows that switching connectors on the graphics card did not fix the bug, which is quite strange. Still the DVI connected monitor shows this bug, while the ones connected via RGB Sub-D->DVI and HDMI do not show it...
Legend:
monitor 1 == left (DVI) <- Launcher mouse hovering detection broken
monitor 2 == middle (RGB) <- working
monitor 3 == right (HDMI) <- working
I have this problem too on my Samsung N310 netbook with 12.10 up to date, but it seems it is not multi-monitor specific: I have experienced it without one.