It turns out there was a bug in the way that the CE 5.0 registry was initialized for hive based registries. This was manifesting itself in DCOM related registry keys, causing them to be garbled and making DCOM not function.
We've fixed the problem in a QFE -- http://support.microsoft.com/kb/904254. If you use DCOM on WinCE 5.0 you definitely should pickup this change. Note this is only CE 5.0 and not previous versions.
Our apologies for the inconvenience this has caused.
[Author: John Spaith]