Saw the same problem here (folders are opened with Totem). Started to happen immediately after upgrading to Intrepid. Yes, I did choose once to open a folder with Totem back then when it was Hardy yet but this didn't change the default: I opened the home folder (and other folders) a zillion times after that and naitilus was started for them, not Totem. What changed the default was the upgrade process.
Saw the same problem here (folders are opened with Totem). Started to happen immediately after upgrading to Intrepid. Yes, I did choose once to open a folder with Totem back then when it was Hardy yet but this didn't change the default: I opened the home folder (and other folders) a zillion times after that and naitilus was started for them, not Totem. What changed the default was the upgrade process.