First let me say sorry to the people that had problems with m3 saves, i only had the one save provided to me to look at, from this i ripped the 400 byte footer and used it when saving any m3 file.
The good thing is your save is not ruined, follow Normmatt's teachings and your save shall be fixed.
I already fixed this for the next version, if you open a m3 file by default it will save your footer automatically and apply it on saving, on the other hand if you open a different t type of save file and save as m3, you will get the static header again, which really can't be helped.
I'll take a look at the jobs in a few hours to see what the problem is, i also added job penalty fixing for the next version + fixing the current job problem, which i hope to get out in the next few days.