Hi Seth,
It sounds like your hard drives might be spinning down when they’re not in use. What this means is that every time you reach a point in your timeline that needs to access footage from a different drive, if that drive hasn’t been used in a while it may have spun down and needs to spin back up in order to get to your footage. This might be the cause of your lag.
If you haven’t done so already, go to System Preferences>Energy Saver and make sure “Put The Hard Disc(s) to sleep when possible” is not checked.
If that’s the case, you might want to consider a larger shared storage option so you can keep all the footage essentially in one place.
I hope this helps!
Michael Nease
Firebare Productions
http://www.firebare.com
Los Angeles, CA