You're counting your rwIndex variable too much each time.
Jesse Seger is on point here. Instead of increasing your line count with one for each true circle that you find, you add one, then two, then three, then four. That can be seen in your movie. This is caused by the way you update both your rwIndex and CheckLoopForHoles index:
CheckLoopForHoles = CheckLoopForHoles + 1
rwIndex = HoleCnt + CheckLoopForHoles + 2
Could one index be enough for this macro or do you need both? If you need both, you can enable the Immediate Window use debug.print to see how these variables change while the macro runs.