Not entirely sure, as we haven't done any big video screenings since last summer (we mostly do outdoor screenings, and it's been too cold for that), and I haven't tried the new version, at all.
But, it was an issue that was present for a long time, and I found a discussion on the mailing list from maybe three years ago when the problem first surfaced. Someone explained that it was an intentional change, but my understanding was that it was only supposed to happen when the video mode changed (i.e. to a different resolution or bit depth). But, we tested it extensively with videos that were identically processed (same container, same compression/encoding, same resolution, same color depth) and it would still glitch. We minimized its visibility by setting the background of the OS to black and hiding all icons and toolbars, which made it close enough to invisible that our clients never noticed it. But, I could spot it, and in an otherwise flawless and reliable experience it was always really annoying.
I'll check the new version out as soon as I've got some free time. We'll need to prepare for the new summer season in a few weeks anyway (we're in Texas, where it gets warm early), and I've been planning to switch to running our videos off of a Linux system, instead of Windows, since I'm finally seeing acceptable audiovisual performance as of the past year or so.
Are you sure those are still present?