If you want foobar2k experts, I'd be looking in hydrogenaudio forums here
or the foobar2k wiki here
Here's a few ideas - Do you have the latest version of the FLAC
codec installed? And the latest version of fb2k? What does the converter status report after a rip say? Did you try their file integrity verifier here
to look at your rips?
I don't use foobar2k for ripping, only transcodeing and playback but did read something about that being a confirmed bug at one time, not sure where now but I would think it's been fixed by now.
2 - I wouldn't set up two libraries as that does create duplicates AFAIK. When I transcode, I have them go to another folder but it's not set up as a library w/fb2k.
3 - I'm not sure about that issue, I've never seen it but could it be possible because you have fb2k pointed at both libraries? Have you tested without having them both on fb2k?