I had the same thing happen to me when I put my FIRST set of new strings on a 35" scale bass, using GHS Boomers, although it was only a 4 string. Turns out the set was an extra long scale set, and regular LONG scale would have fit it properly.
I played out the strings wound up that way, and did not have any problems. Many strings don't have the felt/silk wrap anyway, and you're pretty much winding "string" up on the tuners.
So.. if you have enough wraps on the peg to keep good tune, I would not fret.. well, go ahead and fret, just don't "fret"
Mag...