Had a problem recently with the JDE Adapter (OneWorld) where the devenv send port worked for design time discovery but wouldn’t work at runtime.
Here is the error message (for all that google index goodness)
The Messaging Engine failed to create the transport adapter "JDEAdapter".
OutboundTypeName: "Microsoft.BizTalk.Adapters.JDEOneWorldTransmitter, Microsoft.BizTalk.Adapters.CoreTransmitter, Version=1.0.5025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35"
Exception Details: "Could not load file or assembly 'Microsoft.BizTalk.Adapters.CoreTransmitter, Version=1.0.5025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' or one of its dependencies. The system cannot find the file specified.
The resolution was to switch the BizTalk host from 64bit to 32bit.
A good example of a time when I wish BizTalk would have better error messages.