I know this is an old thread, but I went through this issue about 6 months ago with Stardock's support on the free version (edit: and they didn't have an answer for me other than "Purchase the Pro version! It surely won't have this problem!". Nor did they comment when I provided them with my solution). OP, my computer is configured similarly to yours, I'm sure (I'm guessing you're gov?). It's a certificate issue. Stardock's executables are signed with a UTN-USERFirst-Object issued certificate. Chances are, UTN-USERFirst-Object is not a trusted Root CA or 3rd Party Root CA in your certificate store. Jack187n2's link has instructions similar to what I did on my machine (I can't read German very well, but from the screenshots they added the UTN-USERFirst-Object certificate to one of their trusted CA stores on the machine).
Unfortunately, the certificate Stardock signed the free version with is now expired. I can still run it, but I'm prompted for my administrator credentials every time Fences does anything (startup, log trim, opening the config window, etc). So if you don't have admin access on your machine, this probably isn't a valid option for you. If the certificate on the Pro version is still valid, it may work, though.
You can (probably) view the certificate to see the expiration. Just right-click on fences.exe (in C:\Program Files (x86)\Stardock\Fences) and select properties. Click the "Digital Signatures" tab, select the Stardock Corp signature and click Details. Then click View Certificate. Valid date range should be there. (If you're going to attempt to add the USERFirst cert to your trusted store, from here click the "Certification Path" tab at the top, then click on UTN-USERFirst-Object in the Cert path list, then View Certificate. Click the details tab from there and "Copy to File" to export it for later import into your cert store).
And here's a link on how to add it to your stores if you have admin access: http://technet.microsoft.com/en-us/library/cc754841.aspx#BKMK_addlocal
Note that I really don't recommend doing this if you're on a managed network, especially in a gov facility. Ask your admins; they may be open to adding it for you if they know the possible security impacts and can mitigate them ahead of time.