Could be your SATA Cables are bad or going bad.
I would also update your Motherboard's CHIP Set drivers.
I suggest you open a Asus Support ticket and ask them if they believe your Motherboard needs to be checked if your SATA cables are good.
I have a Asus Motherboard with 4 Internal SATA HDDs installed and I don't have an issue like the one you have.
Now If I am copying a large file like a Windows System Backup file or copying several files at the same time to 2 or more Internal HDDs, My transfer rates slows down quite a bit. In most cases only one or two HDDs are transferring the file and the rest are at Zero Transfer rate until the others finish copying to the other HDDs.
If it is transferring to more than 2 HDDs at the same the time the transfer rate is very slow too all of the HDDs except maybe to one HDD it is faster.