Something to be aware of.
Ok I uploaded a theme with layer and everything was great until I realised that the result within SSA was different for some items within the map.
I compared the theme within MapInfo and it all seemed fine ... it took me awhile to figure out the issue. MapInfo themes are not case sensitive, SSA themes are.
So be sure to correct your data and ensure consistency for any attribute columns you are using for themes within SSA.
Problem solved -- kind of -- Should SSA be changed to match MapInfo or should MapInfo be changed to enforce data consistency?