I got it working. Vikram got me going in the right direction by exporting and then importing the registry keys from a scan I created manually. Apparently, you need to create keys under HKLM, HKEY_USERS, and HKEY_Current_User. I got stick for a little while because I tried to copy (and thought I succeeded in copying) the hex digit created when I manually set up the scans. I used that as the reference for my scripted scans, but when I ran the script, even though the keys were created, nothing appeared in the Endpoint GUI. Finally I realized that I was two digits short for each hex number, and that is why the script was not creating the scans. I added two random number to the end of each, and now it works like a charm.
I don't really recommend this process to anyone - just creating the necessary keys and settings for two different scans under HKEY_USERS bit took about 150 lines of code (and that doesn't include all of the other settings I had to do). But if you have no other choice (as in my case) it is good to know this works.