%pdb magic enables "Automatic pdb calling has been turned ON", but this behavior doesn't actually happen anymore. (In case it's my fault: OSX 10.6.7, system Python 2.6.1, IPython 0.11dev (31c1e49))
I had this (or a similar) problem as well. I tracked down to a failure to import ipdb and was able to fix it by upgrading to the ipdb (to v 0.3). Give it a try and see if that solves your problem.
No, that didn't fix the issue. I imagine it has to do with the reorganized code execution in InteractiveShell.
restore auto debug behavior