You can do VISA communication with multiple com ports at once. You should make sure that your serial vi's are re-entrant. There is a Knowledge Base that discusses the use of multiple serial ports at once (link below). You should also make sure that there is no data dependence from one loop to the next. Since LabVIEW is data dependent, once it has all necessary data, the loop will run. To determine if your loops are running independently, you can turn on "Highlight Execution" mode and see what order things occur in.
http://ae.natinst.com/operations/ae/public.nsf/fca7838c4500dc10862567a100753500/59458684cf7861cc862565410061db3b?OpenDocument
If you are not using LabVIEW, make sure that your application is multi-threaded.
Kim L.
Applications Engineer
National Instrumen
ts