Same issue with Aurei latest in github compiled right now, tried with Rei 3.6b and the update works.It looks like this problem with updates happens only with those apps which get replaced completely when updating.
Tested with Flipnote and Ironfall v1.0. First test build on github fixed it, so I didn't test second one.
At least, Ironfall update is downloading right now, I'll tell if it will be successful or not.