I am not a hardware guy and cannot help much. I just wonder, shouldn't the vblank frequency be 60Hz for NTSC? Yours runs at half speed. As all the following tests depend on the number of vblanks it would explain why your numbers are so far off. As the vblank runs at half speed, these 100 vblanks will last twice as long as expected and therefore the number of ticks per 100 vblanks is almost twice as high as expected, just because it counts twice as long. So IMHO your CIA timers might be ok, your problem is the vblank.
OTOH it is not clear how it measures the vblank frequency. If it uses CIA timers for that, the problem could be the other way round. Because the timers are running too fast, the measued frequency is too low.
