Why are my exported .wmv videos sometimes distorted during the first few seconds?

I am creating 15 second looping motion backgrounds using After Effects CS5 and exporting using Media Encoder. WMV is the only format that is compatible with the programme my clients are using to play them - this is mainly a niche market being churches using EasyWorship, which utilises Windows Media Player to play all videos from, but doesn't support any other codec that WMV.
I am using ccParticle world to produce the particles, using both the default particles (i.e. shaded sphere etc.) and my own either brought in from Photoshop or basic shapes created on After Effects.
I am using fractal noise to give the background layers more depth and texture.
I have made all my looping backgrounds so far using all the features above, making both a HD version and an SD version in After Effects. Some of the backgrounds have exported fine in both formats, whereas a lot, both SD and HD versions have distortion/pixelation at the start lasting for a few seconds.
1080p version export
WIndows media video, 720p - changed the frame rate from 24fps to 25.
SD version export
Windows media video, PAL to high quality version
It is a bit hit and miss whether the backgrounds have this distortion at the start or not... apart from the arrangement and properties of the particles and colour themes everything is the same for all my backgrounds and I am using the same exporting properties every time.
Once again I am probably missing something...
Any suggestions would be appreciated.
Many thanks

Thanks for your reply. I am using a standard preset for the SD export. For the HD I am selecting a standard preset but changing the frame rate. I am not altering the bitrate or any other settings (apart from un-ticking the 'export audio' box). With both I get the pixelation.
H.264 is fine. So I have even tried converting the H.264 file into .WMV just to see if it makes a difference but it still has the pixelation.
For some of my other similar videos I have used exactly the same presets and altered the frame rate on the HD version and had no problem.
I just don't understand why some videos are affected and not others.
I really need a glitch free  HD and an SD .WMV version of the same video that my customers can purchase along with the EasyWorship software mentioned above.

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