What you discribe tends to be pretty standard, but it doesn't hurt to try.
Go to power options under control panel and beside the plan you have selected, click Change Plan Settings, then click Change Advanced Power Settings. Expand the Hard Disk part by clicking the plus sign next to it. Look to see if the Hard Disk is/are set to turn off after a certain amount of time. If the amount of time is equal to or less than how often the video stutters, you could try setting it to never turn the hard disks off and see if that helps.
Also, how often does this happen? You say in your system specs that you have two hard disk. On which one are your videos stored?