Video stuttering, audio fine.  Any ideas or is it just a bug?

I've got a 160Gb box running the latest software. When watching movies which have been ripped with handbrake and are stored locally, they often become a stuttering unwatchable mess. The audio continues to play without any problems though.
These are movies that have played fine in the past and will occassionally play without any problems. However, once they start to stutter, that seems to be them knackered for a while and no reboots will fix the problem.
This problem has been there for a while with the box but is definitely worse since the latest software updates.
While these are movies running from the internal HDD, the box is connected via Ethernet cable to an Airport Extreme which is then getting the rest of its content wirelessly from an iMac which is connected by Ethernet to another AEBS upstairs.
So, any ideas? Its a shame because when the box works its fantastic, but between this and the problem with it hanging on the Apple logo, its starting to become a real PITA.
Thanks.

"While these are movies running from the internal HDD, the box is connected via Ethernet cable to an Airport Extreme which is then getting the rest of its content wirelessly from an iMac which is connected by Ethernet to another AEBS upstairs."
Could be your network setup. If you are using more than router then all secondary routers should be placed in bridge mode(even if using ethernet) then configure wireless settings.

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