sorry, but I’ve no suggestions for your problem. I used OpenAT v3.12 with Eclipse last year for a week and hadn’t had such problems. The only problem which I had in this time was debugging of the simulation — the breakpoints don’t work right.
Under OpenAT 3.13 I work with eclipse too but without the Project wizard — I’m using the commandline utilities instead, That’s not nice, but I can work with with eclipse v3.2 instead of 3.1.