It may not be the same problem, but during my early days with GS, my carefully created templates appeared different when reloading them. I found out that as my sequencer was up and running at the time, the template was changed by the sequencer to whatever setting that had at the time.
Try loading your template when your sequencer is not running yet, and see if all your settings are there for the template.
Now, my template in the sequencer is the same as the template in GS. No changes, unless I change something in the sequencer.
Hope this helps
When opening the GS 3.1 template all seems in order. The problem is still there though when I'm using the sequencer (Logic 7.1). It must be something that Logic is sending to Giga and causing the changes. I'll check it out......