Poor performance when turning HT off

I’m running SLES12 on a dual socket Xeon E5-2699 v3 server and I am noticing a strange behaviour of the OS. When the # of cores are all active and HT is enabled everything seems to be running fine, however when I change (through BIOS) the number of active cores or turn off HT then the OS starts to freeze for a second or so repeatedly as if it were laging however my cpu, memory, cache utilization are all very low.
When I boot up a different distribution of linux, this behavior doesn’t repeat itself.
Has anyone experienced this?

Thanks in advance!