Could be your mag mount. Where the coax goes into the mag mount, there might be a loose connection there. Is it possible to check the soldering under the mag mount? Might not be possible to visibly check because of plastic / rubber covering and don't suggest you break into that.
Another possible cause could be a faulty patch lead. You might be using at least 2 in your set up.
I've had 'dodgey' connections w.r.t soldering inside the PL259 plug, especially if the leads are old and have had lots of use.
Not familiar with you rig and it's SWR controls. Have you got a dummy load? I've found them useful for checking the power output of a rig, and the state of patch leads and power output of rig.
If using a 50 Ohm dummy load and a SWR meter, if you get a 1:1 (ideally) SWR, then at least you know your rig's controls and patch leads are working ok, then the fault must be with magmount and / or antenna.
All the best,