On a development machine, potentially up to 3 versions of the SQLite library can exist in the GAC. An x86 version, an MSIL version, and if you're on 64-bits, either an x64 or Itanium version.
The MSIL version is for compact-framework development usage. Visual Studio needs a pure MSIL version in the GAC marked as "Retargetable" before Visual Studio will do the proper lookup and use the right version of the DLL when compiling typed datasets and such.
When you redistribute your application, you can either distribute the x86 version, the x64 version or the Itanium version depending on your needs. They don't have to be installed in the GAC. If your program is compiled as "Any CPU" and you redistribute only the x86 version of the SQLite library, then your app will fail to load on an x64 machine. So, your choices are:
1. Mark your application as targeting x86 or
2. In your setup program, check for what platform you're installing to, and write the proper version of the SQLite library to your destination directory with your app.
Robert