after a lot of testing with the cygwin installer I figured out the solution to the problem:
I uninstalled libsqlite3 and sqlite3 3.7.16 and installed the sqlite3 and libsqlite3 3.7.13 version instead. Now it works!
I had the same issue and fixed it by upgrading from version 3.7.16 to version 3.8.2.
In other words: Downgrading isn't the only solution, upgrading works too! It's version 3.7.16 specifically that appears to be the problem.