I have the same problem with my incandescents, the signals work fine. I just assumed when they put everything back together at the shop, the contacts were touching somewhere or something was being jumped in a place like the back of the headlight or the ecm needed to be flashed or reset. Haven't really dug into the problem but have been riding with it for weeks.
2012 Highball w/ Power Commander and RPW Big Slash.
2006 Buell Firebolt XB12R Raced mapped/Gutted Exhaust.