You must install the official version of vsix package on sqlite download page (v3.8.0.2).
In the Visual Studio Add-in manager, this package version is 3.7.1.17 and it's not correct.
After, i think it is a bug, you have to select the good processor (platform target).
I had the same error because I deployed a migrated winrt application (8.1) compiled in x86 on a x64 machine... => in windows 8.0 it works, but not in windows 8.1.
If you have a x64 machine you have to select the x64 target compilation. I hope it will be fixed in futur...