In SQL compare (v10 is the one I have), once you've done your table mappings, there is another tab called options. On here under the ignore section is a tick box for extended properties, tick that and then it won't matter if there are different properties on each table.
As @Tarzan mentions in a comment below:
Yes, from SSMS, go to "Tools > Options > SQL Server Object Explorer > scripting > Script extended properties = False".