file you are looking for cannot be found

create a batch file to re-map the network drives...
eg:

@echo off

Net Use Y: /Delete /y
Net Use Y: \\192.168.1.254\SharedFolder1 adminpassword /USER:adminunsername /y

Net Use Z: /Delete /y
Net Use Z: \\192.168.1.254\SharedFolder2 adminpassword /USER:adminunsername /y

Save it in the Startup folder of the client PC, and create a shortcut to it on your desktop if you want.

how does this differ from a regular mapped drive and what might cause the shortcut to the executable that did work, suddenly not connect again, if the program were closed, then reopened?

it doesn't differ from a regular mapped drive, it's the same just done with the CLI rather than GUI.

Drive mappings will sometimes disconnect after 15 mins of inactivity.  
To fix this (in XP):
http://support.microsoft.com/kb/297684#appliesto

On the server you may need to change group policies:
Start>Run>gpedit.msc [ENTER]
Expand Computer Configuration>Windows Settings>Security Settings>Local Policies>Security Option:
Microsoft Network Server:Amount of idle time required before suspending session.
Zero (0) will disable it
.

 

would it be common for server group policies left unedited to frequently "disconnect" program shortcuts causing annoying frequent reboots. And is it possible that mainstream applications would automatically adjust the group policy timings to avoid such system tweaks manually?

yes to the first and no to the second.
The default timeout for disconnecting idle connections is 15 mins.  This is standard for almost all Windows OS installs.
Mainstream applications are usually intended to be installed in the environment they are most commonly used in, which is stand-alone systems with normal network setups.  If the program was designed to run on and rely on a network, it wouldn't use mapped drives for this.

the program in question was written. The program was not assembled as a typical installed type software, but simple compiled into a regular folder that was placed on the server. These issues I have explained have only been occurring since the folder was copied to the new 2008 x64 server. The old server was a 32 bit. It was confirmed by the software maker that the compiled program would run fine on a 64 bit server.

You can try disabled SMB 2.0 on your server.  i would also update any firmware on your switches.  that can cause the issue too.

I'm not too sure how the installer was compiled and what system changes it could have made to the 32 OS that failed to occur on the x64, but if the batch file fix (which really just recreates the mapped drives on log in) and the GPO and registry tweaks fixed the issue, then it is quite likely that the installer (not the program) was built correctly for the x64 OS.
Is everything running OK now?

all viable options worth working with. Very helpful.

Well, I believe I discovered what my issue was on one of my PC's. I thought that we were all experiencing some new issues with the program since we had installed Symantec Endpoint AV Clients. After uninstalling the Symantec, most of the issues disappeared. I installed MS Essentials AV. I was still unable to double-click the shortcut and get the exe to launch on my PC. I ran a full scan on my PC to find that I had 10 instances of Exploit:Java/CVE-2010-0840.W. None of the other AVware: Symantec, Sophos, AVG or Avast identified the problems including Malwarebytes. After they were removed, I rebooted, rescanned, rebooted and the program launched multiple times. Its been fine ever since. Another small program, autoruns.exe from MS helped me remove some old removed program remnants that I was never able to get at. Uninstall usually doesnt uninstall everything. This lesson in frustration lead me to try extremes. Normally I would just reformat and reinstall the OS which is why I never store anything on the C: drive except the OS and programs. Sometimes the damage goes too far and reformat is the only option. Only time will tell if the recovery was successful.