Yes, saving at the ice cream factory messes up your chances at getting 100%. I didn't know about the "ice cream factory curse" and I had to do it all over again. It only let me have 99%, just to tease me. Chances are, if you did all the jumps, rampages, hidden packages, races, everything and still end up with 99%, you must've saved somewhere wrong and will have to do it all over again.
But be sure to check a list online to see if you've forgotten something.
This save thing kept happening to me so in all, I've gotten 99% about 4 times, and finally when I saved safely at only a few select places,on my fifth try I got 100%.