It is difficult to say without knowing the person or context. Some people just think differentely about words. So, when I say a paper was "nice" I mean "that was really satisfying and heart-warming to listen to", but some people might mean "that was average" or even "that was slick."
For me, personally:
"that was fine" = yup, okay, you fulfilled basic requirements, but no great insight / excitement.
"that was good" = one-up from the above, fulfilled basic requirements and a bit more besides / or that was better than might be required. Still room for improvement, though.
"that went well" = that was a success - no slip-ups and a positive outcome.
Also, bear in mind that crusty old-school academics can be notoriously reticent about giving praise. I once had a paper accepted for publication, which my supervisor had said was "fine". Heh.
Hope that helps.