This is a user to user message and not an official response.
I ran into a lot of problems with having 1.2005.1 and 2.0 both installed at the same time.
Make a copy of the 1.2005.1 dll's and use them as browse to assembly references instead of using the GAC for other projects not yet upgraded. Note: Once you upgrade a LGP file to 2.0, there is no going back, but I haven't found the need to. 2.0 can still generate 1.1 dotnet code if necessary.
Then remove all versions of LLBLGen.
Then install the latest full version and your new 2.0 license file.
I don't think it is actually LLBLGens fault, it appears to be more a problem with the way that Visual Studio 2005 keeps assembly version references in the sln file.
I spent most of a weekend trying to upgrade a multi project solution and kept getting weird compiler errors until I finally did the above.