I hate that message! I have a batch file set to run via a timer and every day it stops because it wants to verify the publisher.
Here is a way to disable the message:
1. Click Start–>Run and type gpedit.msc. Click OK
2. Go to User Configuration–>Administrative Templates–>Windows Components–>Attachment Manager
3. Add “*.exe” to the “Inclusion list for moderate risk file types” setting. You can also add other file types.
This should disable the “Publisher Could Not Be Verified” messages from appearing for that file type in the future.
(Note, this is the second method I’ve used for this and I’m waiting to see how well it works. I used a different method yesterday via IE to trust the directory where the batch file is located and it made absolutely no difference at all)