After Effects rendering a video at base 99, but outputs as a 60 one
Since your source is in h264 I'm guessing you are encoding to mp4/h264 again?
The format doesn't support a frame rate of 99, you will have to use a less constrained video codec like mjpeg in an avi or mov container.

Whenever you are violating certain video or audio specs After Effects will tell you that in your export settings like shown here (see the little warning triangle in the left corner). AME doesn't do that for some reason but will show the adjusted settings in the source output info field.