I didn't see this in the compiled list of suggestions:
I have responded to 2 or 3 posters with the same problem - residual data in the XSEQ file from when they change Timings and then Save. The sequence in the Nutracker screen will correctly show the change, but the Preview window looks wrong.
The reason is that the change left the old pixel data in the XSEQ file while creating the new pixel data in the new time slot. The fix is to insert a "Color Wash - Black" in the time before the change, and that erases the old pixel data.
While that works, perhaps you could put check box above each Model's column to "Clear Before Save" to erase that Model's pixel addresses before saving?
For people who program ENTIRELY in Nutcracker, this would be pretty safe.
BUT, this could be dangerous for people who are mixing sequencer programs (like I do). For example, if I was adding effects to an imported LOR sequence, I might erase some LOR data that I did have in that same Pixel space. I've only done that once and had the LOR data protected by using "None, None" in the time range I was protecting.
Perhaps the "Clear Before Save" could watch for that? That's about the only reason I've ever used "None, None" in a sequence.