AVCHD 1080/50i export to mpeg 1080/50i - video stutters

when exporting the complete sequence to mpeg 1080/50i the resulting video stutters at 2 to 3 points. Thus I exported 3 parts of the sequence: no video stutters. Then I create a new sequence based on the resulting 3 videoclips, export the complete sequences and the exported video stutters again at some points.
Can anybody help?

What version of Premiere Pro? ==> PP CC
Have you installed the recent updates? ==> yes
What operating system? ==> Win 7 Professional SP1 64-Bit
What kind(s) of source footage? ==> AVCHD 1080/50i
If you are getting error message(s), what is the full text of the error message(s)? ==> not relevant
Has this ever worked before? ==> yes, has been working for smaller export files (less than 120 seconds)
What other software are you running? ==> nothing in parallel except security & firewall SW
Do you have any third-party effects or codecs installed? ==> No
Tell us about your computer hardware. ==> 6 core CPU 3,4 GHz, 64GB RAM - 6 GB RAM for other applications
Are you using Mercury Playback Engine GPU Acceleration? ==> yes - NVIDIA Quadro 2000
Does the problem only happen with your final output, with previews, or both? ==> only with the final output - the preview is fine - combining the shorter files (up to 120 sec) to one big sequence (4 min) --> the final export is stuttering at some times (even the export of the shorter files was fine)

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