Allen,
I've run into something like this before, where a binary (.exe) file that was not in one of the TestStand Search Directories would get 'lost', while other files in the exact same directory where found by the deployment. This appears to have happened because the binary file was was not referenced with an absolute path, while the other files in this directory where using absolute paths. When the build was migrated to the Configuration Management build machine, the TestStand workspace 'lost' the file. Our workaround was to make the binary files path absolute.
The deployment utility did not throw a warning that it could not find a file in the workspace, and just omitted it from the deployment when it was built. So we ended up with Engineering builds that worked, but a CM release build that didn't. If the deployment tool did throw an error message, it was lost in the several dozen warning messages that where also thrown (we deploy sequences that reference several separate binary DLL's that aren't deployed as part of this particular deployment, and use expressions for sequence paths and sequence names).
Even though it performed an analysis, it didn't clearly warn that one of the files in the workspace environment had a problem.
Hope this helps...
-Jack