Once you know what DRAM Clock Fine Delays to use with the Memory it doesn't really matter what slots you use.
Yes, MemSet V4.0 is an excellent program. I hope Felix adds Auto tREF in a next version that calculates tREF according to JEDEC specs for the Memory speed that is used.
To change tREF and automatically load it on the next boot all you have to do is set the tREF timing you want, apply it and save.
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