Apple has deprecated MCX since 10.7. I am still wondering why some MCX kept working in 10.10.
I would really recommend to use profiles instead. If it's a .command or something like you wrote, you can even use a login policy instead of MCX. In short, there are a few other ways but using MCX is a bad idea.

Thanks MIchael, yes i know MCX is not the preferred way to go. I only have a few Managed Preferences like the disable Natural Scroll option and just a coule extra. I never could get those to work with profiles.

My concern is why they all of sudden stopped working. As I mentioned I used to see the dialog that is was applying managed preferences but that is not showing. How can I tell if the JSS is pushing out the Managed preferences?

So, I just confirmed that installing the Papercut login hook disabled the ability of the Managed Preferences to be received and applied. Anyone have a suggestion to where I might be able to correct this? Maybe a permission issue?

This also broke the script I had running in one of the labs as a policy to give a user a message at login. Other policies seemed to be loading fine as well as profiles.

I tried to run the uninstall command for the login hook but it does not help.

The only Managed preferences I had were:
Disable Natural Scroll
Auto Logout after 60 mInutes
Open last window dialog unchecked

I know these seem trivial but I get complaints from the students and faculty. If I could get these to work with profiles, that would be great but I can;t seem to get the Natural Scroll to go that route.

Any help would be greatly appreciated.

Well with the help of support figured out the the PaperCut login hook install overrode the JAMF login hook settings. Running sudo jamf manage via terminal got it back to use the JAMF login hooks.

I then have a script running as a policy to launch PaperCut at login.

@grecopj glad you got it sorted.

Was going to chime in with this article, as seems like in this case 2 is not better than 1.