Well, this is an old thread that I only found because I'm looking for the thread that has the list of all the "Space Quest" fan games (I thought there was such a thread but now I can't find it), so the original poster probably either found the solution already or gave up a long time ago. But for anyone else having the same issue:

First of all, I think this is actually a "Space Quest 6" issue not a "Space Quest 5" issue, since the only thing I can think of that would relate to this is the Endodroid in SQ6. Yes, putting him in the freezer does get you extra points. Yes, this extends the time you have before he escapes for a little bit. But only a little bit. You have to take him out of the freezer right away and hurry back to the guy who was trying to catch him. If you take too long during any part of this puzzle, he will return to form and kill you.