Hi Marek,
Go to "Project -> Render", in the presets choose "ffmpeg" then "Edit", in Video Section take "Options" and then choose "Initial RC complexity" or "Initial RC buffer occupancy" or "Quantizer compression" or "Quantizer blur" or "Luminance masking" or "Darkness masking" or "Temporary complexity masking" or "Spatial complexity masking" or "Border masking" or "Inter block masking".
Besides - there is new version available: http://sourceforge.net/project/showfiles.php?group_id=142766
This bug is still present in version 0.0.20080523 compiled from source. It's well worth upgrading though.
Cheers! Daniel