Yes. The same thing has happened to me. I have moved uni to do my masters and I really dont like the place at all. However I really needed to go somewhere else for my masters as the facillities at my undergraduate institution were not good and therefore my lab skills and research experience would have been really limited if i'd stayed. I can't say I regeret going because I had to move on.
So all I can do is say that its only for 1 year and then I can go somewhere else for my PhD, which I am doing. But it's not easy.
Was it practical for you to stay at yr undergrad institution?