Were your downriggers sitting for a while before you changed from wire to braid? I had a similar problem earlier this year the first time out. Basically, the counter was spinning too fast on the way down so was over counting. I think the grease or whatever provides some friction in the counter had dried up over winter. Or maybe the unspooling / spooling in quick succession had the same effect.
You can check by opening the cover and flicking the counter wheel with your finger - if it spins freely (i.e. counts off more than a foot per flick) you've found your problem.
Fortunately, it is an easy fix and takes about five minutes - find your nearest Scotty dealer / service provider and they can get you a new counter, should be about $20 - $30 (unfortunately you can't take the counter, it is a sealed unit).