I justed wanted to follow up on this issue. I found the solution to the problem by accident. I was going through the menus on our dimmer packs and accidently changed the dimmer pack to 8 dimmers. As a result the unit also changed to single phase. I changed the settings back to 12 dimmers and 3-phase. After that when I tried our light board all the lights connected to this dimmer pack worked properly (faded gradually like they are supposed to). I repeated this "procedure" on the other 3 dimmer packs and it fixed the problem we were having!
Now I don't know why it fixed the problem. I know that the displays said 12 dimmers @ 3-phase before I made this change, but it must have reset something internally.