Gems => could it be they have different values?
Arrows => in earlier versions some arrows had different values. When I patched, they changed their names but didn't stack. Example (made it up now) => 7 poison arrows of the viper - after patching to 1.44, they changed to simple poison arrows, but did not stack with the other ones.
so, did you patch and get the info: "BD has detected a prob with your save, click yes to fix it"?
