It's all working fine except for the second hard drive which is extremely slow (~2-4MB/s) when reading / writing /deleting large numbers of files at once.
Both hard drives are SATA 3, and connected to the two SATA 3 connectors on the motherboard.
The primary (boot) hard drive with Windows on is working fine - rapid read / write of files as expected.
On the second drive, the speed drops to ~4 MB/s or less when working with multiple files. For example, a 2GB folder containing ~20,000 files takes over 40 minutes to copy on the second drive compared to under 2 minutes on the primary drive. For single large fies it generally starts fairly fast (~30MB/s) then drops to around 10MB/s or less. General use read-write on the drive is also very slow - I've been trying to run an XAMPP server on the drive and it's reguarly breaking PHP's 30 second timeout when loading very basic web pages.
I've tried a few things already:
1) Killed anti-virus
2) Removed drive volume and re-created
3) Turned off Windows file contents indexing on the drive
4) Drivers on the system are all the latest versions