We use mandatory profiles to lock down the accounts. I have an application that needs to be run as an administrator to function. Is there any way of for one application to maybe put a shortcut that runs it as an admin without asking for any other password that will enable users to run that program as

Hi,

Did you meet any issue with Lync? If yes, please elaborate the issue.

From your description above, it can be a issue about Windows client, you can post a case on Client forum and there are more experts will help to solve the issue:

https://social.technet.microsoft.com/Forums/windows/en-US/home?category=w7itpro%2Cw8itpro%2Cwindowsvistaitpro%2Cwindowsxpitpro%2Cwindowsintune

Best Regards,
Eason Huang

Yes Lync to connect needs to add a cert to the personal store. With mandatory profiles the users don't have permission to do this. If I run the program as admin it works but I cannot do that for thousands of students and the certs store isn't like a folder I can just allow permissions to, or at least I haven't found out how yet.