haha was just posting this issue, seen this also.

Found an easier way to make the saves work, only skimmed this thread so apologies if this has been mentioned. I use 2 profiles the default one and Will695.

in C:\Users\%username%\Documents\Arma 3\Saved\steam
find the mission and copy the .pbo

go to

C:\Program Files (x86)\Steam\SteamApps\common\Arma 3\Missions

and paste the pbo's in there (i subscribed to a load of missions as today was the 1st time I've played any scenario's)

when in ARMA Scenario's you'll now see 2 lots of the same mission,one under a steam "tree" and the other just above. Use the ones not in the steam tree and you'll get a resume. Bit of an easier way than saving the save.arma3save and renaming every time. you don't have to worry about it.