Using quicktime 7.6.9 h264 compression_flicker is introduced

Using quicktime 7.6.9 h264 compression_ a flicker is introduced into one scene in my film -- tried multiple settings, and getting the same issue.  Color and brightness shift between frames  -- but only in 1 shot/scene. 
Using quicktime version 10.1 (exporting file to PC/Mac compression) produces a beautiful picture quality,  but it changes my frame rate from (source 23.98 fps) to 23.90 fps!! I would love to keep the frame rate matching my source @ 23.98.  I"ve never heard of 23.90 as a frame rate. 
Any suggestions on either front would be most appreciated!!!!

hello Jeff and Colin,
thanks for commenting...
would you have any information on the fact that:
"""maybe it's the quick time that's been killing me all along
because (i just remembered this) when i use ccleaner the error logs
are always regarding qt32 stuff?""""
i am away from my desktop station until august 11 so i can't get you actual log files,
but i'm pretty sure what was happening was that PPRO would hang on editing when applying effect (including NEAT VIDEO
(which i know needs a lot of juice)
and then i would kill the process, or i would close PPRO and it wouldn't close in TaskManager,
the funny thing is is that after i'd kill the process and reopen PPRO, the effect would be 'rendered' on the timeline
(even the NEATVIDEO)...
however, it wasn't until being bored that i was really reading everything that CCLEANER was cleaning.
i have it set to clear out the error log files and lo and behold most of the log files were regarding QT32 stuff...
this is why i investigating everything i can about QuicTime's interaction with CS5 5.03...
thanks again for helping,
j
perhaps it's the effects that are crashing QT32???

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