UPDATE - I've made some progress in figuring this out.
It looks like I've got two problems:
1) The LSI controller should be reading from both drives in the RAID 1 VD but sometimes decides to only read from one. I can reproduce this on WD Se drives and WD Red drives.
2) The WD Se drives, even when connected to the motherboard, get angry when hit with two long read operations at the same time.
With regards to problem #2, consider the following test when connected to the motherboard's controller and reading large (10-15 GB) files
A) WD Red, one read process: Read rate is 150 MB/s
WD Red, two read processes: Read rate is 140 MB/s
C) WD Se, one read process: Read rate is 180 MB/s
D) WD Se, two read processes: Read rate is 10-15 MB/s and drive makes growling sound
I've put in a call to WD to see if there's a firmware update for this drive. I got to Level 2 support but apparently there's only one Level 3 guy and he was out today so I'll try again tomorrow.