I have two Harmony 680's and have one of them set to control my Fortec FTA box. Works fine, but I did have to learn some commands manually into the remote (such as SAT and SIG).
One quirk I noticed was this summer when my portable AC unit (rollaround type with hose to window, I believe it's a GE) responded to the Harmony's Fortec commands as well (but not if I used the original Fortec remote!!). It got to be a little confusing to have the on/off timer on the GE changed every time I flipped channels on the Fortec....
I recently tried to get my other Harmony to control my Pansat 3500, but either the Harmony database has the wrong codes or I did something wrong.. Will be playing around with it again this weekend.
Hope this helps,
Robbert