SQLite extremely slow: Windows vs. OpenBSD

I read a lot, I know Stackoverflow is full of SQLite speed problems, I tried a lot of thing, but nothing worked. And also mine is a little bit different.

So here is my problem: I have an average PC (with i3 cpu) for developing, really nothing special. (windows os) I have to work with SQLite database files, and on my PC I have really no problems. Queries are fast, I mean which one must runs in 1s it does, which one need 5 secs, it runs in 5 secs. But! The same java code, with the same SQLite queries on our company server (this server has an OpenBSD OS) run EXTREMELY slow. I mean a 1s query runs in 30 s, and a 5s query runs in 30 min(!!). Unacceptable. I really tried everything: using transactions, not using transactions, add indexes, drop indexes, using different joins, changing my queris, I tried different JDK-s, only running on the server, and buliding too on the server, but nothing helped: in every case on that server the queries are slow. I have no more idea why. Can someone give me a tip about this?

Of course I have 'suspects', but not facts. One is the OpenBSD itself. And also it seems to very slow opening (or connecting to) these database files, but mostly these are just feelings.