TW3 - "Set Overall Mod Priority" Settings Reverted Upon Next Deployment

[Zanderat]

....as the topic says. If I use the Script Merger to set priorities for mods, shouldn't those changes reflect in the load order screen? When I deploy, any changes made are undone. Very frustrating.

[Zanderat]

I plan on filing a bug report, but need to know if this actually a bug or intended behavior (and thus user error).

[Zanderat]

Bug report filed. This can't be right.