I've never had trouble skipping that event. (And I've skipped that event loads of times, because I usually re-load my save as soon as we get back to the shop.) That sounds like a pretty weird problem. How reproducible is it?
If you want weird though, I once had to save in town, because I forgot to save in the shop, then I went dungeon diving, got killed, re-loaded the save, and STILL didn't have the items I brought with us into the dungeon.