Stuttering in Rendered Output

I am having some problems with the rendered output from kdenlive.

I am using H264 lossless (fast) preset, with mp3 audio. (aac caused the rendering to stall at a certain point each time, any light on this would also be good!)

But my main problem is that the rendered output stutters slightly in some places, mainly around the position of transitions/composites.
There is no stutter when playing through the project window, only in my media player after rendering. I have tried multiple media players, (totem/vlc) and both do it in apparently the same places, leading me to think it is the video file that has the problem.

I'm away from my pc at the moment but can provide system specs/software versions later if they are needed.

Forums:

Fedora 16
Kdenlive 0.8.2.1
ffmpeg-libs-0.8.10-1
mlt-0.7.6-3

Note: this version of ffmpeg is updated since I posted my original problem, but the issue still persists.

No one able to help with this?
Through reading other posts it MAY be a bug in ffmpeg?
Is someone able to help me with the procedure to downgrade ffmpeg to a version it might work with?