Linux – Ubuntu Monodevelop not starting, gtk-sharp missing

I'm just switching from windows to ubuntu, just that you know I'm a linux noob.
I've compiled monodevelop (4.0) from sources, because only the old 2.x version can be installed with apt-get. Then my project didn't run, because there was no VB.NET compiler for .NET 4.0. So I thought I'll just compile the new Mono 3, too (only 2.x can be installed with apt-get).

Mono soruces downloaded, compiled, installed, seems to be working:

$ mono --version
Mono JIT compiler version 3.0.12 (master/e4a5774 So 9. Jun 12:41:41 CEST 2013)

But now monodevelop isnt starting anymore, over my desktop icon nothing happens, then I looked what it returns in the terminal:

$ monodevelop
System.TypeInitializationException: An exception was thrown by the type initializer for     Mono.Unix.Native.Syscall ---> System.EntryPointNotFoundException: Mono_Posix_Syscall_get_at_fdcwd
  at (wrapper managed-to-native) Mono.Unix.Native.Syscall:get_at_fdcwd ()
  at Mono.Unix.Native.Syscall..cctor () [0x0000a] in /home/manky/Work/mono/mcs/class/Mono.Posix/Mono.Unix.Native/Syscall.cs:2168 
  --- End of inner exception stack trace ---
  at MonoDevelop.Core.LoggingService.RedirectOutputToFileUnix (FilePath logDirectory, System.String logName) [0x0001e] in /home/manky/Work/monodevelop/main/src/core/MonoDevelop.Core/MonoDevelop.Core/LoggingService.cs:177 
  at MonoDevelop.Core.LoggingService.RedirectOutputToLogFile () [0x00041] in /home/manky/Work/monodevelop/main/src/core/MonoDevelop.Core/MonoDevelop.Core/LoggingService.cs:140 
FATAL ERROR [2013-06-09 13:27:54Z]: MonoDevelop failed to start. Some of the assemblies required to run MonoDevelop (for example gtk-sharp)may not be properly installed in the GAC.
System.IO.FileNotFoundException: Could not load file or assembly 'gtk-sharp, Version=2.12.0.0, Culture=neutral, PublicKeyToken=35e10195dab3c99f' or one of its dependencies.
File name: 'gtk-sharp, Version=2.12.0.0, Culture=neutral, PublicKeyToken=35e10195dab3c99f'
  at MonoDevelop.Ide.IdeStartup.Main (System.String[] args) [0x0005c] in /home/manky/Work/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Ide/IdeStartup.cs:533 

But i've double checked if gtk-sharp is installed. Also:

$ ls /usr/lib/mono/gac/gtk-sharp/2.12.0.0__35e10195dab3c99f/
gtk-sharp.dll  gtk-sharp.dll.config

I tried to recompile monodevelop, but now it isn't compiling anymore, it seems like it can't find the gtk-sharp and gdk-sharp libraries now, too.

So I don't know what to do next. This problem is driving me crazy, I just want to get monodevelop with VB.NET 4.0 on my Ubuntu-System to work. Can somebody help me?

EDIT: So I uninstalled mono and monodevelop and installed the official old versions for ubuntu, and now its running again. But can someone tell me how to remove the old mono version and replace it with my new compiled one?