Not lately. Check the "group" definition, where the DelayMin=, DelayMinInterv=, and SpawnProbability= lines are, and see if they are set correctly, as lurker had in his original file. Even just looking at things in the ME can re-set things - especially the first line, as you're well aware. I include the SpawnProbability= line, since they're not all at 100%, though I think the Shinano was... you weren't too close to the spawn, correct? No alternate route scripted in? You didn't do like me and mis-number the groups with an addition, did you?...
One time, it "blanked" the file. You'd never know it from the game, since there's so much else going on, but when I went to use the MIS file for a "merge" for reference to where other RGG were placed, there wasn't anything to see... a blank file, even though they were all in the text, the ME couldn't display it. I don't remember if that was a double, like two Group 200's, or if I skipped a number or what... or maybe it was in a groups' RndUnit definitions...