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I've never had that problem with medialink- the only setback I encountered was the DRM on files downloaded from iTunes.
 
You're probably using incompatible settings. Just because it's MP4 doesn't mean it'll play.

Did you pick the PS3 preset? That should select all the proper settings.
 
Medialink updates are free. Just redownload Medialink from www.nullriver.com.

Do you own QuickTime Pro? If so, you might try "badging" the Handbrake files you create by exporting them within Pro to MP4 (select passthrough on video and audio).
 
i do have pro but cant find passthough

does badge recreate the file?

"QuickTime badge" is just a phrase. By exporting to MP4 through QuickTime, it creates a standard MPEG-4 wrapper. Other programs don't always create MPEG-4 files that are standards compliant.

The PS3 is very picky with regards to this.

File - > Export - > MP4

Then select the following options (no transcoding or re-encoding will take place), then save:
 

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