I came across something an issue yesterday when upgrading a BizTalk Server solution to run on BTS10 which is sitting on Windows Server 2008. The solution has a custom itinerary resolver and from within the itinerary resolver a call is made to the registry to retrieve some config.
Sticking my toe in the water I configured a host to run under the local admin account as 32 bit only. In this configuration the registry calls failed. I took at look at the registry to see if it had been locked down with some kind of funky permission set in WinSvr08 but nope, still by default local admin has full access. So I stepped through the code and found everything was correct. The code could see the HKLM hive and the SOFTWARE subkey but nothing below that.
So I reconfigured BizTalk to use a 64 bit host and hey presto it works first time and every time. For a desciption of why 32 bit didn’t work see the following KB, http://support.microsoft.com/kb/896459