you really shouldn't have that issue.... and if it is happening on your MDs as well then it isn't your core hardware unless it is related to the disk and/or network subsystems.
I would start by putting such a file on another system (a PC, NAS, or something else) and adding that to your LMCE network. Once scanned in, ask one of your MDs to play the media.... this eliminates the core as the MD connects directly to the PC/NAS and reads the video from there. If the problem stops then it is likely your HDD in some way given that the network is not involved in replay on the core, from the core.
What format is the HDD on the core? Its not ntfs is it? And the problem continued even after a rebuild?