Weird Behaviour after transferring to new pc case - Makes no sense

Hoping someone can offer the solution or a direction in which to look, as my issue makes no sense.

Yesterday I transferred my system to a new tower case and switched to a liquid cooling system.

Once assembled and checked I connected everything and turned it on, all went smoothly and there were no errors reported. But I soon became aware something was not quite right when I open up the file explorer, I was used to it seeing it open and populated in a flash, especially given my C drive is an SSD. But this time it opened, took several seconds to populate the left panel and several more to populate the right side. If I clicked on anything I noticed the message "Not Responding" in the title strip. I then started testing a few other applications and quickly noticed there were some that would start as they should and other simply will not open up.

I used CPU-Z to check the CPU and memory and both reported speeds and settings exactly as they were in the old case.

The BIOS reported the CPU ticking along at 37degC.

The only thing that I am aware that has been changed is that my SATA drives are not plugged into the same sockets as they were in the old case. I did not think this important, I thought with SATA it did not matter. But in doing a search of this site and forum, I did find a similar issue and someone suggested changing SATA sockets, so is it critical?

Important main System specs are
ASUS SABETOOTH X99 MB
Samsung 1TB SSD as C Drive

In closure, I am regretting touching the system, it was flying along and rated very highly in comparison bench mark tests, now I seem to an old DX4-100 system.

Any suggestions most appreciated.
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