You're using the main black heatsink that covers the entire card? Unlikely that the switch is overheating. There is plenty of thermal mass to dissipate heat.
It's hard to help diagnose what is going on with little information.
What drives are you using in it?
What MacOS are you running?
Are there other PCIe cards in the Mac Pro right now?
Are you doing a RAID10 through SoftRAID or AppleRAID?
What are you using to measure the performance?
A few tests that would help you narrow this down:
1. Try a RAID0. Just for testing. Does the same oscillation occur when you stress test the drive? If you are using SoftRAID, try in Apple RAID as well.
Use AJA to test. 4k full, 16 bit RGBA, 64GB file size.
ac Pro 2019 and Mac Pro 5,1 is merely PCI 3.0 vs. 2.0
Of note: On a Mac Pro 5,1 when you use PCIe 4.0 drives, they link/revert down to PCIe 1.0 (I know, oof). PCIe 3.0 drives link at PCIe 2.0 speeds.