To left-align the free note card section, add this line just before the final "}" in your cart customization code:
ejejc_jQuery("#tdPmnt").attr("style","font-family:Verdana;font-size:11px;text-align:left;width:100%;");
I tried unsuccessfully to reproduce the issue you described with typing in that field, sounds like perhaps your computer briefly had trouble connecting to our server at that moment when you were testing.