Manual mesh levelling Z-values gets reversed on print

So I just flashed my firmware with the JyersUi and got me a 5x5 manual mesh leveling on my ender 3 v2. Somehow my prints came out even worse than before, so I thought maybe something is up with the mesh leveling. I tried giving the printer absurdly high z-values between 4-9 mm(positive numbers). I saw the z-axis go up to the specified value and went on to fill the mesh with these random numbers, just to see if it actually used the mesh when printing.
Then, when I started a print my nozzle just drilled in to the bed like there was no tomorrow. Did my Z-values get reversed upon saving the mesh somehow and is this a known issue?

I have entered M420 S1 command in my slicer and saved the mesh to EEPROM

First thing to do is adjust the Z end stop switch or the bed to ensure the switch triggers (home = 0) when the nozzle is still above the bed. The gap needs to be less than any 1st layer thickness you may want to use.
The bed leveling systems help calculate what this distance is and try to keep it consistent across the bed.