I have had ha similar issue with the caret. In my case I found that it was caused by having two copies of the same file open in Mono-develop at the same time.
Annoying that I can have two copies of the same file open at the same time mind, but closing one of the duplicate copies resolved my jumping caret.
For me (Mavericks, Unity 4.5), all these annoying issues still exist: MonoDevelop doesn’t jump to the error lines, doesn’t open solution automatically when opening scripts from Unity, text glitches, random changes of keyboard shortcuts (cmd+a builds the solution instead of selecting all text, works again after restart) etc… None of these issues existed on OSX 10.8 / Unity 4.2