Well, the whole thing is worse than I thought, and I'm sure it is all related to the horrible mess Linux makes of file associations and the like. Since I upgraded Calibre and my plugins yesterday, I can no longer open some file types, like tar or zip, from within Chrome - it launches Calibre. Open the same file from nautilus, no problem.
I think I'm just gonna reinstall my OS and everything this weekend. Thanks to all for suggestions, I did try them without success.