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Give the details of your configuration, machine components,project settings, etc. Far too vague for an answer, otherwise.
Xeon dual quad E5345 (2.33GHz) on a Tyan Tempest m/b. Vista 64 bit, 8Gb RAM. Sata RAID 5 array with 6 WD raptor HDD for the video array - many other system and cache disks.
Project is Sony XDCAM EX 1080p (HQ) but also happens on other HD sequences.
I was after whether generally anyone has seen this behaviour before in-depth trouble shooting.
Which other HD sequences?
XDCAM HD sequences too (1440x1080)
Both GOP media.
Do you get the same issues with I-frame only source media in an appropriate sequence?