Privileges For Executing Custom Drive Mapping Executable

[dccsp92]

I am curious to know what the execution privileges for a custom executable are when being called from route-up or up flags? I have a custom app that requests a users credentials and domain to map a series of network drives based on an xml file containing the mapping information. I can't just script the drive mappings since many of the home users are not on our domain and/or are not savy enough to know how to login with a domain account. I use this application and it maps and unmaps the drives fine provided I call it directly. When I run it from the route-up flag directly or via a batch file, it will say it will succeed but it never actually will map the drives. This has to be some permission issue. I have tried changing the script-security from 2 to 3 and adding system but nothing works. Is there a way to run a custom application like this?
Thanks in advance,
Dan