I run x2 980 ti's and don't have this issue. The game does support SLI, I know you said you only have one card. However, the game runs at a max of 90 fps by default anyways. So I don't see how much more you can limit it. That should work though, you can use MSi afterburner to limit fps, or nvidia profile inspector (you have to download) to limit the fps. Maybe when you limit the fps you only do it for the default swat 4 config file and not the tss one. Look at the swat 4 pcgamingwiki page on how to limit your fps. It might not be saving to the folder or something. I use msi afterburner to limit my fps in games so try that.

The bigest problem with UnrealEngine 2.x games and servers is that Frame Rate, Tick Rate and Netspeed are entanglement.

Those 3 distinct roles are synchronized, what causes a lot of inconvenients.

For example, I will point 3 situations to limit your Frame Rate, and its downsides:

1 - Limiting FPS turning V-Sync On, in Swat4.ini;

Result is that either Networking Packets per Second and UnrealScript Interpreting Cycle (tickrate) will be also capped to 60.

2 - Limiting you Netspeed, choosing values like 5000 (Modem 56kbps), 4000 or even 1800;

Result is that your your will suffer during FPS drops, and tickrate will again slowdown game script execution process.

3 - Limiting CPU speed ("C:\Program Files (x86)\GOG Galaxy\Games\SWAT 4\Content\System\Swat4.exe" -cpuspeed=2000), thus limiting tickrate;

Result is that your your will suffer during FPS drops, and also networking will be affect again.

Honestly, I still use 4:3 pattern - 1280x1024X32@90Hz. That's helpful during FPS drops.

and, yes. "DesiredRefreshRate" is useless.

Download Nvidia Inspector (just google it, get it from guru3d - 1.9.7.6 latest)
click the button next to the driver version
At top under profiles, select SWAT 4
Under "2-Sync and Refresh" note "Frame Rate LImiter"
Set that to whatever value you want it at.

Have fun!

Go into Nvidia control panel and switch on Vsync from there at driver level.

I had the same problem - enabled Vsync in Nvidia control panel and all was well ;)