Hi Chris,
Apologies for not getting back to you sooner. I also don't have great news on this. This is an issue that I have seen intermittently on several builds of MDT servers that I have done. I haven't spent a huge amount of time trying to debug it but in the time I did spend looking, I wasn't able to spot what was going wrong.
I did update the script to use an INI file but that was only to read in default settings, it didn't alter how this writes entries to the MDT database. The relevant field in an entry in the database, is the task sequence. When I looked, that field seemed to be populated correctly, so currently I don't know why that isn't being used properly.