How do I get a lip sync flash frame sequence to encode properly

I built a flash frame sequ
ence in Premiere.  It is 2 seconds long with the
first two frame white and the remaining time black
frames. This is repeated for 1 minute.  If I encode it in non-compressed AVI it is correct.  If I use
MPEG2 or H.264 to build a transport stream, I see two white frames
as I would expect,then black frames for the rest of the sequence.  Over 15 seconds, I will start to see three frames, gray, white and gray again.  Eventually, the white or gray frame starts two frames later than it should.  I built this as a 720P/60 sequence with non-drop frame timecode.  I have tried all I frames and the same issue occurs.  The GOP structure does not seem to have an effect.  There is no audio in this stream.  It as if it cannot handle the quick and short transistion from white to black.  There are some advanced settings for MPEG 2 but I cannot see where they are explained in the Premier help document.  I need this stream to measure latency on a piece of video equipment.
Thanks
Ralph

Bill,
Your answer gave me a hint to what was happening.  I'm fairly new to Premier and took for granted that the preset I chose at the begining of the program would carry through to the sequence, wrong!  I found another discussion that talked about resetting the properties of a sequence.  I expanded the project box a little and saw that it said my sequence was 59.94 frame rate not 60.  I followed the instructions on the other discussion.  File, new sequence, general, editing mode, and frame rate.  The frame rate was set to 59.94 not 60.  I reset it to 60, closed all the menues and deleted the original 59.94 sequence.  The new sequence I just created shows a 60 Hz frame rate.  I exported my lip sync project as an MPEG 2 transport stream and it was correct according to our MPEG analyzer.
Thanks again for the help.
Ralph

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