Thanks for your post.
The internal way that SQL Compare works out dependencies is not something I'm aware of in any detail (it's pretty complex!)
In general it gets things in the correct order; but occasionally certain databases will cause trouble, especially in situations with circular dependency references and so on.
I'd be interested in a couple of tests though- firstly; can you test it using full permissions on both databases as described here
? It may be that the reduced permissions on one of the databases are having an effect.
If that makes no difference, does the GUI behave any different to the command line? There's a couple of issues under investigation where the commandline sometimes yields slightly different results, and you may be encountering this.
If neither of the above help it may well be a problem specific to your DB's - if you're able to send snapshots (create these on the File menu) to us, referencing F0064853 in the subject line, we can see if there's anything obvious.