sdi clocks and computer video output clocks are NOT locked together -
all clocks drift all the time - its not a buggy software or a hardware issue -
its a genlock thing- video systems use a common clock for video synchronisation-
in n546 theres a pseudo genlock catalyst framerate from phoenix input one sdi clock
which sets the catalyst playback frame rate to the phoenix sdi clock time ( approximately )
we just used this to deal with problems on queen tour
the sdi system clock was 25.001Hz referenced to the computer video output clock - big enough to cause glitching like you describe