Certain videos play poorly in PlaceShifter

[VCRUser]

Please bear with an explanation that might be long-winded. I have several videos from PlayOn that I have run through Handbrake to compress and then copied to my server. The videos look fine in the following environments:

Server ui on main server (Computer 1)
Extenders (200 and 300)
Placeshifter 9 (installed for testing on one of my other computers: Computer 2)
VLC on Computer 3

They don't, however, look right on Placeshifter 6, which I use on Computer 3, which is my main tv-watching computer because it runs under Java 6 and still has the video always-on-top working (apparently, that option disappeared with Java 7 and subsequent). For use on that computer, video always-on-top is pretty important, since I'm usually doing various other things on the puter while watching videos.

This is just a few videos, all converted with Handbrake (but only a small subset of the Handbrake conversions, though I've been discovering more and more that exhibit the problem, and so am motivated to find a solution. While going forward, I can do more testing to discover which Handbrake settings do and don't produce video that is acceptable to PS 6 (and make sure it's ok before deleting the originals), I need to be able to enjoy the ones on-hand. The problems I've seen so far include:

Video with partial loss or distortion of color. While watchable, it's not great.
Video that looks like an old analog tv that's not tuned very well - kind of zigzaggy. This isn't watchable at all.

I have already tried fiddling with the Placeshifter settings and fiddling with the video settings on the server, with no change.

It occurred to me that I could try installing PS 9 or even Client 9 on Computer 3 for use just for the problem videos. The concern I have is that doing that will install Java 8, potentially rendering PS 6 with Java 6 unavailable. I did try copying the installed files from Computer 2 to Computer 3, but it complains that it needs Java 7 or higher. On another system, I apparently had some success with tricking it into thinking Java 6 was Java 7 by renaming a copy of the folder. No such luck now.

A wrinkle: My PS6 is 32-bit, and the PS9 I've been trying to experiment with is 64-bit. Is it possible to have a 32-bit Java 6 used by PS6 and a 64-bit Java used by PS9 and they would all live harmoniously together? If so, that could solve my problem. I'm just nervous about setting anything up lest it somehow causes me to lose my alway-on-top capability in some irrecoverable way. I've copied the folder in which the current Java runtime lives, and have installation files stashed, so I would think I could recover if need be, but still...

For those who have read this far, thanks for any ideas - either regarding fixing my PS6 setup in some way or setting it up to live happily next to a PS9 "special occasion" version - or to get the latter to run always-on-top so I wouldn't need to keep 2 versions around.