MD, I do agree that it seems improbable given a standard barrel but perhaps it is a replacement barrel. There are other ways to get bullets to be unstable but they take some effort to make happen. Loading exceedingly cock-eyed cartridges, a poorly throated/chambered barrel, damaging bullets when seating/crimping, etc. might do it. My suggestion to look at the crown is another. MD, you can probably come up with 20 other ways to get a bullet flying cattywumpus as well.
The symptoms you describe are a dead ringer for the problems we so often in BPCR and esp. BPTR where we are always pushing the bullet weight to the limits over excessively long range. Faster twist barrels, shorter bullets, and sometimes more velocity (if possible) generally fixes the problem. But whether this is likely with your M99, I don't know.
I'd sure like to see some close ups of the bullet holes in the cardboard from the 100 and 200 yds targets. If they are less round at 200 yds, then bullet stability IS the problem. Finding the cause of the problem may, however, be problematic.
