Well i downloaded your 2 vi's and left mouse button clicked and held down, etc. and i did not see either vi stop counting, or any pause at all.
I'd suggest to try setting the time critcal vi to highest priority, and maybe the other one to lowest priority. If that doesn't work, try cutting out all unnecessary code and indicators and only use globals and locals if absolutely necessary (see performance tips in LV help). If you still have problems you may need to upgrade your computer, clean it up (delete unused programs/files) or reformat/reinstall.