^ So I gave it a try myself, and I always kept the item inside my inventory after using it, with a cooldown of 8 minutes. Give the re-uploaded fix a try, maybe it fixes your other issue too.
Some changes were made to Noitalacse Island and Where the Time Goes — basically the ones mentioned here. You can get the patch for the Faster Leveling (N) version here: [Download]
I have uploaded fixes for both Dawn of Masteries compatibility patches, in addition to the changes above tokens should now drop too. Get them from the update page. I completely rebuilt the Faster Leveling (N) / Non Lightweight version, which hopefully ensures that everything works correctly.