Hello Mark,
The first thing I would look into would be memory. If you are on a low end laptop I am assuming you do not have much memory. LabVIEW eats up memory real fast when you use Globals. Not only is there a memory location taken for the global, but each time you call it in the VI you are making a new copy of the global, therefore a new memory location it taken. That could causing the other parts of the program to slow down, like the counter timers skipping.
I hope this helps,
Doug