Sorry - been busy lately and I missed this...
I use HVPro, but have the same issue. There are a couple ways to resolve it:
1) Program your controller so when links are issued, they update the light values to the new states. The downside to this is that when you program or change a link (in upstart), you need to go to your controller and update the new link values there as well (or they won't match).
2) Issue a update status command out of your controller (a standard UPB command). It will issue a request to the switch and return the current value of the switch. I've created a macro that goes through all my switches/modules and gets their current value. The downside to this method is it takes time to get all the values (I think I set it to use .5 seconds between switches so it takes some time to go "around the house"). So far, the time delay has not been an issue - my touchscreen displays "updating" when it's occuring so a user would know it's occuring.