Of course, this was to be expected.
I use Random Altermate Start ( http://www.nexusmods.com/skyrim/mods/25404/? ), and I selected the New Game option, totally expecting it to conflict, and it, indeed, does.
Of course, disabling one or the other bypasses this problem, and I don't know if it can be fixed, but I just figured it could use some attention, as there are lots of people that use alternate start mods.
I'll try it out with some others as well.

#1
This has been said many times, it is even on the FAQ - you should have read that. If you find this inconvenient maybe you should make a compatibility patch.