Running executable files - which is the best way?

Is it best to operate three of the same re-entrant vi files from three independently running executable files or is it best to run all three of the same vi files from a single instance of labview?
I have a re-entrant vi that I created with NI Developer Suite 2006, V8.2.  I saved that vi as three different named vi files for the purpose of creating an executable file from each of them.  These executable files control three identical devices via three serial ports from a USB to serial port hub.  The executable files are run simultaneously on one laptop and they do operate for the most part as expected.  There is a concern about 1 possible IRQ conflict (best guess is that two of the three com ports might be using the same IRQ; com5, com6 and com7 are being used) because one of the three com ports didn't appear to be passing commands as expected like the other two ports did when I first started running the vi.  I'm using a separate port monitoring program to view the transfer of commands to and from the device conected to the serial port to show me the command code being generated to the device and received from the device to validate the proper operation of the executable vi and to time stamp the transfers.
/BCU002
Hardware Engineer•Design Reliability/Performance and Validation Group•Wavecom, Inc. - Research Triangle Park, N.C.•http://www.wavecom.com

Megan,
Thanks for the reply!  First I want to answer your questions.  I do have three independent executables operating simultaneously and each one has been assigned it's own Com port.  The text file is intended to time stamp the ADC reading every two hours.  Each UUT has it's own file that documents the ADC value independently.  I do this to validate the operability of the UUT during the test and doing so also shows me when the UUT fails to operate.  However this problem that I'm havinig with the VI has been providing me with misleading results about the durability of the UUT and I can't figure out why it happens after 12 hours.
The UUT is  working okay.  I checked Friday it and reset the program and the power to it and it's been running ever since through the weekend.  However the one problem that remains consistent is that after 12 hours the readings for the ADC, which is what I use to verify that the unit is transmitting RF into a dummy load while in factory test mode, just start showing up as 0 when they should be in the high 100's.  One of the UUTs has an RF power meter connected to it's RF antenna and it's been working as expected when I start the test I have a software engineer running the exact same test on the same type of UUT using an entirely different software tool and it's not having any of these symtoms after running for days on end, uninterrupted.  Unfortunately I can't use that software tool for my work because I can't control it with Labview...yet.
I'd be happy to email you a copy of the VI that I created directly if you think that you can look over it to see if there are any design problems that I need to repair.
I've attached a compressed file containing a bitmap of the control panels that I use during my test and I've included two NI spy files for you to see what's happening while my VIs are running and the 3 text files that recorded all of the ADC readings from the UUT over the weekend.  I hope you have the time to look at them because  can use the help.
/BCU002
Hardware Engineer•Design Reliability/Performance and Validation Group•Wavecom, Inc. - Research Triangle Park, N.C.•http://www.wavecom.com
Attachments:
FTM Control 123.zip ‏467 KB

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