The games aren't made by Stardock, so you can run into incompatibility issues. Fences Pro is coming this week (Wednesday, I think) but that's not a free program.
Stardock doesn't do support for the free programs...it's an "as is" thing (logical, since you don't have infinite manpower to service free stuff).
So, if you wish to have both programs, I'd suggest you buy Fences Pro, and get all the support you need. If not....
Features of Fences Pro: Link.
*edit: As of today, Stardock will support Fences 1.0. Try uninstalling it, and reinstalling via Impulse. If it still 'won't play well with others', open a ticket at Tech Support at Stardock.