Asagrim,
From our point of view it’s good to hear that there doesn’t appear to be a bug in our plugin, though that obviously doesn’t help you. I mentioned cygwin because of the format of the current directory showing in the Terminal+ view. It seemed like a Cygwin format (below cygrive, e.g. /c/…), though I see there may be other possibilities.
If your other IDE also uses git-bash, it may be worth checking there for some settings that may affect this, though I can’t say what they might be and I doubt you’ve changed anything (the git-bash implementation is under .webclipse\git-bash in your home folder).
Without your particular environment, it is difficult for us to recommend anything or try to track it down here but I’ll mention it to the development team to see if they have any suggestions.
If you find a solution to this, we’d be grateful if you’d let us know as other users may come across the problem and we may be able to account for it, within the plug-in, in the future.