Effects: Level settings not rendered correctly in export

I am having the following issue in Premiere Pro CS5.
I have an image sequence with alpha placed over some film footage. The sequence is supposed to blend with the real footage.
To do so, I have adjusted the sequence with a few effect filters.
The filer setup is as follows:
- levels
- shadow/highlight
- fast color corrector
- levels (this one is added later for just a little bit extra control)
In the program monitor it looks great, and the preview render on the timeline looks good. However, after exporting the media, the effect filters seem gone, or at least different from what it is supposed to be.
Anyone familiar with this problem?
Thank you,
Robert

Thanks for the replies. Unfortunately the issue is not solved yet. Like Colin expected, it's already set to software (The option "GPU Accelerated" is disabled).
Some specs:
- It's an 720p24 project
- the overlay is an PNG sequence with alpha
In the export render settings "Use Maximum Render Quality" was selected. But deselecting it, gave the same result.
In "Sequence settings", the option "Maximum Render Quality" is also selected. What's the difference for these 2? Is it worth a try to deselect this option aswell?
Any thoughts of what it could be?
(if helpfull, I will try to post some screenshots of the problem)
Thanks

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