Hi Stomp,
Which silicon are you seeing this on? (part # and silicon revision).
There was an issue with revision A silicon on some of our products, with an interaction between reset and power domains. I think this is in an errata, but I have one of these boards on my desk and it's a problem quite often when debugging and issuing a system reset through the debugger. If you have this silicon the best answer would be to get the latest silicon version.
Let us know.