The first thing to check is that you have the latest AHCI/RAID drivers for all brands of disk controller on your board... with matching latest firmware.
Firmware RAID needs matching/compatible drivers for the code in the firmware.
With old BIOS we used to replace RAID code modules into the BIOS ourselves when ASUS dropped/slowed support, not sure what happens with this new type of firmware, so keep in mind you may need to track when/if drivers become incompatible over the years. (or keep an eye out for someone with the code base). Hopefully it will be supported for long enough though.
Whatever you do DO NOT update disk controller drivers through windows update. Always download it yourself and read the readme(s).
For example for GENE-Z you need to track this...
http://downloadcenter.intel.com/SearchResult.aspx?lang=eng&ProductFamily=Chipsets&ProductLine=Chipse...and this (eSATA so does not matter as much)...
ftp://driver.jmicron.com.tw/SATA_Controller/Windows/...keeping in mind what controller versions are in the bios at any time.
The second thing to check is defrag, windows will protect certain parts of the disk from fast access at certain times and defrag will reduce the likelihood of generic benchmarks hitting these sections at the wrong time. There are one or two benchmarks that know where these sections/files are and avoid them (like PC mark), most other benchmarks just pick parts of the disk sequentially or at random so this can cause the above effect as well.
Check driver versions and firmware first though.. last thing on earth you should do is defrag with wrong driver ;oP (also a good idea to backup before changing drivers and firmware.. especially if you change the controller mode from AHCI to Raid or something like that.)