Try to redownload it?
Personally, Endless Nova is one piece of nice fanwork. I spent about 10h till I went through (without every single quest, though there aren't that many besides the main plot) but I'm still trying to kill this darn Watcher Omega. Even Fusion Quenlin and Paradorn haven't been a problem at all (thanks to Atlas), but that Wather Omega kicks my behind. Am trying to raise my HP and Mana to about 1000 points which takes quite a long time - but I'm fanatic
Of course Endless Nova isn't as professional as the other FF games, but since it has been programmed by one single person, the plot being dense and capturing, the simple but addicting "equip your char with new items every here and there"-system, a whole bunch of enemies and very detailed areas I really enjoyed playing this one. I loved playing FF II on the Gameboy a few years ago and this one reminded me of it at once. I really like it, though it's quite diverting.
I really think it's not as bad as Matango considers it as