I performed the tests on two different arcs. The arcs were created on a Windows Vista machine, then transferred to a Windows XP machine. The first arc had no custom characters or groups, the second had custom characters and a custom enemy group.
On the first arc:
testArc (16.17% = 13,981 bytes)
ArcA-vista (16.17% = 13,981 bytes)
ArcB-xp (16.17% = 13,981 bytes)
On the second arc:
testArc (*% = 118,655 bytes)
ArcA-vista (100.37% = 126,262 bytes)
ArcB-xp (92.48% = 118,627 bytes)
The percentage for testArc matched that of the arc saved on the particular machine.
Doing a diff on testArc and ArcB-xp showed the only difference to be a BossAnimation (ChickenTug) was removed in ArcB-xp. That's because testArc was created while ChickenTug was still a valid animation and it got automatically removed on loading testArc.
Doing a diff on ArcA-vista and ArcB-xp showed that ArcA-vista had a custom character that I had removed from the VillainGroup for the mission.
The critter and cvg files for the custom character and villain group on the vista machine still show the character I had removed from the group as still being in the group, but testArc and ArcB-xp did not have the character in them.
The problem seems to be that the critter and cvg files get reloaded if they exist on the machine, even if they no longer match those in the storyarc file.
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@Mass Transit
(The friend with the house-of-many-computers)