I had this problem every time I deployed a new website or updated an existing one using MSDeploy.
I was able to fix this by unloading the app domain using MSDeploy with the following syntax:
msdeploy.exe -verb:sync -source:recycleApp -dest:recycleApp="Default Web Site/myAppName",recycleMode=UnloadAppDomain
You can also stop, start, or recycle the application pool - more details here: http://technet.microsoft.com/en-us/library/ee522997%28v=ws.10%29.aspx
While Armaan's solution helped get me unstuck, it did not make the problem go away permanently.