I believe it is because the newest change (in the multi mod) overwrites previous changes. I had similar issues, for example with Ultra switched back to +2 armor instead of +4. In editor it was +2, test map - +2, but on bnet it was +4. In the end I replaced the upgrade with a custom made one (a carbon copy), but then same issue happened again with something else.
Switching around the order of how different dependancies were loaded solved this issue completely.