What sort of issues did you hit with version 2 on Linux? I'm playing around with it now and rather like it, and the fact that the open source is in C# (which I know intimately) doesn't hurt. So I find that I actually care about this question, and need to give some thought to whether the Linux problems are killers for me.

(Version 1 is certainly an option, but version 2 is considerably more feature-rich, and some of those features are interesting to me...)