I just wanted to share some information just in case someone else comes across this issue and is scratching his/her head. I experienced an issue that seemed random until I looked deeper into it. It started with an injections form we use that was translating the same field twice. For example, the NDC was translating in the NDC section and the Manufacturer section. Looking into it, I saw that in the .xlt file, there was a duplicate global variable created for two different OBS terms.
After talking to Logical Innovations, it turns out that my development VM is too fast and the algorithm they use to generate the variable names is time-based. They sent me a "dirty" executable for testing purposes, but there is not a permanent fix yet. I have temporarily resorted to developing on a 32-bit machine again. I'm assuming the 64-bit architecture we moved to is the reason it is "too fast."
Interesting... what are the specs of your VM that make it too fast?
Windows Server 2008 R2 Datacenter SP1
(2) Intel Xeon X5660 2.8 GHz
8GB RAM
64-bit