Gilligan

One of two things are happening:

Normal INS drift. Over time the INS system builds up small errors over time called "drift." The longer you fly, the more errors stack, the further off your SPI's will appear vs the intended terrain markers. The INS system in the F16 is "GPS corrected," so if you are flying with the GPS enabled after a certain amount (IIRC about 300 meters) of drift accumulation the GPS will attempt to "correct" this error but it can still be a couple hundred meters off. 
 
The second thing that could be happening is that you are offsetting your SPI via one of the sensor systems like the TGP, Ground Radar, or HAD/HTS. Take the TGP for example, if you slew the cursor off the steer/mark point you have selected and initiate a point/area/INS lock on a location, there are X, Y, and Z offsets to that point relative to steer/markpoint that are automatically stored and  will be applied universally to all other steer/mark points. To cancel out or "zero" out this offset, use the cursor zero function either by pressing the corresponding MFD button, or by using TMS down short. 

How are you boresighting the mavs? on the ground or in the air? I have a much better correlation if I do it in the air at max range.

I would try setting the boresight off the destroyed mortar site right at 8 miles or so. 
 
Once you establish the point track on the truck with the TGP, try zooming out a bit so it more closely matches with the view you get with the Mav seeker. Start your attack run at about 15 miles out so you have time to line everything up.

Single Flare, No intervals just spamming the counter measure switch down button.

Once you've created the markpoint, set it as the current steerpoint and TMS down to "unlock" or zero out the cursor, then re-set your lock with the area track.
 
You can also use TMS down (once the cursor is unlocked) to set an INS track - similar to an area track but even less likely to lose the lock point when maneuvering.