I know I’m late to the party but I had this issue right after I pulled down latest x86/x64 today (version 18.104.22.168). My local IIS in VS2012 runs 32bit by default and there’s no easy way to switch to x64. My production server runs 64bit.
Anyway I installed the NuGet package to a DLL project and I got this error. What I had to do to get it working I had to install it to the main site project, too. Even if it doesn’t touch SQLite classes at all.
My guess is that SQLite uses the entry assembly to detect which version of Interop to load.