This was touched upon in the following thread:
http://www.ootpdevelopments.com/boar...em#post2170344
It appears that when you import a schedule it orders the teams by numeric team_id. When you export a schedule it orders them alphabetically by team name. If these two different sorts result in different orders, importing and exporting the same schedule will cause teams to be switched around in the schedule.
I know there probably won't be any more patches for the current version, and this issue can be worked around, but hopefully the import and export functions will be uniform in how they determine the order of teams in the schedule for the next version.