strange InvalidCastExceptions from NSObject to NSBundle/NSUserDefaults with mono runtime 2.10.12 - xamarin.ios

Question

I seem to be having some problems after updating Xamarin/Monotouch this morning.
I updated MonoDevelop to 3.06 from whatever version was current and stable 10 days ago (sorry I can't be more specific), and Xamarin Studio to 4.0.2. I've been using MonoDevelop exclusively and have opened Xamarin Studio only now, wondering whether or not I was encountering a MonoDevelop bug.
My current MonoTouch version is:
Xamarin.iOS
Version: 6.2.1.201 (Enterprise Edition)
Hash: ed9807c
Branch:
Build date: 2013-19-03 13:42:59-0400
In either IDE, when running my app in either release or debug mode in the Simulator my app crashes with following InvalidCastExceptions:
System.InvalidCastException: Unable to cast object of type 'MonoTouch.Foundation.NSObject' to type 'MonoTouch.Foundation.NSUserDefaults'.
System.InvalidCastException: Unable to cast object of type 'MonoTouch.Foundation.NSObject' to type 'MonoTouch.Foundation.NSBundle'
These aren't the sort of casts that I'd expect to have fail on me :-)
In any case, the app compiles, transfers and runs correctly on an iPhone 4 with iOS 6.1.2 when built and installed from either Xamarin Studio or MonoDevelop
I've set the runtime target to 2.10.12, 2.10.11 and 2.10.9 (via this new Runtime Target menu option in the menus, even though it's meant to have no effect), and each time the app crashes in the same way.
This is all on code that was working correctly before the update (last week, before I went off to Iceland for a holiday and nobody touched anything while I was gone)
We don't use any third party assemblies; I've cleaned and rebuilt all assemblies but that hasn't helped. I'm about to try to narrow the problem down in a small test solution.
UPDATE 1:
Looking at the assemblies' version numbers in MonoDevelop, I see:
Assembly Version 2.0.5.0, found in /Developer/MonoTouch/usr/lib/mono/2.1
Monotouch has an Assemlby Version of 0.0.0.0.
I created a new MonoTouch project and added the first offending line to its main method:
public class Application
{
static void Main (string[] args)
{
// My real App crashes on this line with an InvalidCastException:
string s = NSUserDefaults.StandardUserDefaults.StringForKey("Login");
UIApplication.Main (args, null, "AppDelegate");
}
}
This ran fine.
UPDATE 2:
After changing the Build Options of the test app to match what we have in our real app, I get the same crash. The build options we have are:
iPhone Build -> General -> Linker Options -> Link All Assemblies
iPhone Build -> Advanced -> Use SGen generational garbage collector
iPhone Build -> Advanced -> Use SGen generational garbage collector -> Use reference counting extension.
Disabling ("Use reference counting extension") allows both the test app and my real app to run without crashing. So the problem seems to lie there.

Answer 1

I've updated to Xamarin Studio 4.0.2 and MonoDevelop 3.0.6
So you updated MonoDevelop 3.0.6 to Xamarin Studio 4.0.2, right ? Sadly that does not tell us exactly which version of MonoTouch/Xamarin.iOS was used before/now.
The easiest way to get exact version information is to use the "Xamarin Studio" menu, "About Xamarin Studio" item, "Show Details" button and copy/paste the version informations (you can use the "Copy Information" button).
Could you edit your question to add this ?
my app crashes with following InvalidCastExceptions:
Do you use pre-built assemblies ? If some were against MonoTouch 6.0.x (or earlier) then the strongname change (in 6.2.x) could result in two different monotouch.dll being loaded - and you won't be able to cast instances between them.
If everything is rebuilt from source (no 3rd party .dll that can't be re-compiled) could you try to make a small sample (e.g. by reducing/commenting parts of your app) to show exactly where this happens ? (if possible edit your question with the source or file a bug report).
I've set the runtime target to 2.10.12, 2.10.11 and 2.10.9
The installed system mono is a requirement to run Xamarin Studio and some tools. However application built by Xamarin.iOS does not depend on the system installed Mono. IOW Xamarin.iOS ships with it's own runtime and SDK libraries (e.g. assemblies).