Unlikely the factory drilled holes are the issue.

There have been some issues reported with the weaver bases for 99's in the past although I have never encountered them myself. My money is on the bases being the problem.

"You cannot invade mainland America. There would be a rifle behind every blade of grass"
~Admiral Yamamoto~

When the people fear their government, there is tyranny; when the government fears the people, there is liberty. ~Thomas Jefferson~