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.

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.
I must have overlooked it. No need to get sassy, I was just trying to help.
Actually, I'm not sure that telling anybody that Skyrim specific mods don't work here is really that helpful. Guess what? Mods that strengthen dragons aren't going to work here either.
If you want to track down mods that don't work with Skywind, please look at mods that "should" effect all game play, no matter what location your player is in. Things like perks, skills, etc. I've already discovered that new versions of spells have been recreated here. Therefore a mod that changes the original Skyrim version won't effect Skywind's version.
Cordicuss wrote:
1.) Deactivate your alternate start mod in your mod manager.
2.) Launch Skyrim.
3.) Select 'New Game'
4.) Select 'Morrowind'
5.) After you get off the boat and finish Character Generation save your game and exit.
6.) Go back into Mod Manager and re-activate alternate start mod.
Or are you expecting your Random Start Mod to drop you in a location that it isn't even aware exists yet? In that case, you'd need to contact Syclonix. But since the mod hasn't been updated over a year, I wouldn't hold your breath.
Jesus, what's up with the responses here. The guy was just reporting that a mod didn't work well with Skywind. I wouldn't exactly agree with posting it as a bug, but no need to be so aggressive with users.