Paul (and others), You probably already know this, but it bears repeating. The loft algorithms change every release, and sometimes between service packs. To keep data safe, SolidWorks retains all of the old algorithms and uses those for legacy data. In SW2004, if you edit a loft made in SW99 it will rebuild using the SW99 algorithms. If you delete the loft in SW2004 and re-use all the sections, guide curves (ick), etc. to remake the loft, SW will use the present algorithms. So, in theory, the loft can't change unless you delete it and remake it. In practice, I'm sure that somebody (my bets on Paul Salvador because he's really good at finding these things) has examples where the rules fail. But that's how its supposed to work.
-Ed