Here's my two cents. I have a reproducable and similar issue with my Carbonite outputting to a couple Christie Digital HD20k-J projectors.
Switching from computer source to an internal source, whether by fade or cut would cause a momentary sync loss.
The following workaround solved my problem: Strip out the ancillary content from the console. N strip was sufficient. This is only a minor issue for my setup since we reembed the "show audio" downstream of the switcher anyways.
From the setup manual:
To Strip or Pass Ancillary Data
1. Press MENU > SYSTEM > NEXT.
2. Use the Anclry knob to select whether ancillary data is stripped or passed.
"¢ N Strp "” ancillary data is stripped
"¢ N Pass "” ancillary data is passed unmodified
"¢ L Strp "” ancillary data and some lines of active video are replaced with black
"¢ L Pass "” ancillary data and some lines of active video are passed unmodified
#Carbonite