Just got a tumbleweed badge for this question!
I spent 2 days solid getting geronimo to talk to eclipse, this problem disappeared at some stage while fixing another one. I still get a warning when I run geronimo, but have chosen to ignore it and get on with life.
It amazes me that something that should be so simple, can become so damn complicated.
If anyone is searching for the same problem, I think (not 100% sure), it came about because I installed geronimo under c:\geronimo, then under c:\g when I re-installed it in an effort to ensure the path name for the longest path name was short enough.
Anyway, good luck :)