It has never happened to me and I also got the reverse gear recall done. I am wondering if when they disabled the reverse module something was done to the linkage that now has the shift mechanism misaligned or something and somehow affects the second gear downshifting but not up shifting?
May not be related but some owner have complained about the reverse gear not engaging and the R symbol flashing on the dash. The answer/work around has been to rock the bike back and forth to release the tension and then it works. This wasn’t because the reverse gear recall, it seems to affect some bikes more than others, maybe the first edition ones, I can’t say for certain. Mine thankfully never does this. I believe it warrants a further investigation. If you have a go pro or similar device that could take a video when you downshift and share it, not only as proof to Motorrad that the issue is real but also maybe someone here could offer a better explanation.