Yeh, I think you're right about the MXI icon - that only gets used by Extension Manager.
I would look for your extension in the service manager folder (on a Mac if you've installed with EM then that'll be in /Library/Application\ Support/Adobe/CS6ServiceManager/extensions/your_bundle_id, if you're running locally then it'll be under the user Library folder; for Windows I think it's under
C:\Program Files\Common Files\Adobe\CS6ServiceManager\extensions\your_bundle_id). You should double check that the icons are there, and that they're in the right place (CS6ServiceManager/extensions/your_bundle_id/icons/Normal.png).
I think I'm near to the solution, but I'm afraid I'd need some extra help.
I've found out that EB's visual editor for the manifest didn't update the actual xml file (so that the editor showed some icons path and the actual xml a different one). Then I've compared the two manifest.xml (the one in the .staged-extension hidden folder and the one in the bin-debug/CSXS folder) and found discrepancies there as well. To tell the truth, even the .mxi (in the extension version) resetted to 1.0.0 - that's maybe because I've messed with an external text editor directly with the xml and mxi while FB was open...?
Anyway, I've uninstalled with Extension Manager the extension, synchronized the two xml, fixed the mxi. Exported the ZXP, with certificate and timestamp.
Before installing it, I've checked that both:
/Volumes/Macintosh\ HD/Library/Application\ Support/Adobe/CS6ServiceManager/extensions
were empty (at least my extension was *not* listed). Just in case you're wondering, /Applications/Adobe\ Photoshop\ CS6/Plug-ins/Panels is empty as well.
To my surprise, if I launch Photoshop, here it is - my extension. Mind you, the folders are empty and I haven't installed the ZXP yet. How could it be?!
So I'd like to get rid of that before installing the possibly-correct version; but... how?
I finally got it. I've worked too much probably, but believe me those folders were empty and the trash too... And I'm a teetotaler :-)
(I did also a test deleting my extension in CS5.1 - same result: empty folders but running panel)
I've restarted the machine and for some reason the files appeared again where they weren't supposed to be. Got rid of them, installed the extension and bingo!
I'm quite sure it was a problem with Finder - and for the broken icons the blame is to put on the mis-synchronized xml, I guess.