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Can you try this custom build and see if it solves the problem for you?
I'm pretty sure I've fixed the bug illustrated in screenshot #2 (the iPhone Bundle Signing settings dialog bug), but not sure about the core issue.
I've changed MonoDevelop to use the Common Name when signing as opposed to the thumbprint.
Your custom build solved the "Unknown Profile" problem. :)
I still have problems with Application Loader (I've attached the Application Loader Screenshot).
I've attached the output.
Could it be a problem outside MonoDevelop?
Well, anything is possible... but I think it's reasonable to suspect that it's a MonoDevelop bug somewhere, I just don't know where.
Do you happen to know if this ever worked with a prior version of MonoDevelop? Perhaps that might provide some clues if it did...
I was just playing with Xcode 4.4.1 and it does not appear to add the binary magic bytes to the beginning of the .xcent file, so perhaps they have changed the format.
I'm working on a fix to drop the binary header from the .xcent file when the user has Xcode >= 4.4.1 installed. I'll upload a new custom build once I finish. This might be the problem...
Okay, new try at fixing this bug: http://files.xamarin.com/~jeff/MonoDevelop-126.96.36.199js2.dmg
This version won't write the binary magic to the beginning of the .xcent file since Xcode 4.4.1 does not seem to use it (at least some older versions required it, but Apple seems to have changed this recently).
Might not be the problem since the codesign utility might handle the old format with the binary magic at the beginning, but there's only 1 way to find out.