I'm running a series of rather large databases from which remote users (traveling salesmen) connect to. Because these databases don't function too well through Remote Connection, I set up a Dell Server that runs Terminal Service (allowing the processing to be done locally).

It works perfect; however, the salesmen often run a script that sends an email containing information pulled from fields. This is where the problem occurs.

The salesmen use Mac computers, the Terminal Service is PC. Since they are connecting to the Terminal Service, it runs the script and opens Outlook Express instead of "Mail" (the Mac equivalent).

Is there something I can do to run this script to use the Mac Mail app.?

No.

Except for configuring Outlook with a generic account and emailing a PDF to the sales guys so that they can then forward it from their Macs to the recipient.

Or using the FM10 feature to use Send Mail through SMTP directly instead of through a mail client.