Deleting the custom entires fixed it here as well! Thank you.

I can confirm that my machine that was reporting incorrectly is now reporting the correct OS after removing the custom entry in the inventory collection.

I just had to do this on our system as well.

Same issue with 10.10 and 9.25, except I had to remove a custom path from the Plug-Ins collection.

This issue still exists in 9.61. Removing /Users/ from the Application inventory scan solved it for us.

@bvandepol,
Wow. This has been a problem for me for a long time. Thank you for posting this information.

After reading this thread and removing all custom paths, the problem still existed (9.61 JSS). I grabbed a screen shot of the various inventory items we were collecting and then disabled (unchecked) all of them. BOOM. The recon finished perfectly. I then started rechecking the settings one by one and re-running a recon. The following option caused inventory collection to fail on my 10.10.1 machine.

Collect last backup date/time for managed mobile devices that are synced to computers

I was also able to add back our custom /Users/ path on the Application inventory scan as well.

I'm seeing that, in relation to this issue, I have machines that are checking in to the JSS but not sending inventory updates. I've tried re-enrolling and that doesn't help either. We don't have that "Collect last backup date/time" thing enabled, but I'll try disabling and re-enabling the other inventory collection options and see if it's hanging somewhere (good catch, @sacomsto).

Appears to have been addressed by the latest update to the JSS, version 9.62, according to the release notes. Anyone gotten a chance to check it out and see if this helped?

I just updated my JSS to version 9.62 and can confirm the issue I was seeing with Inventory Policy not being able to search /Users/ is now fixed...

I can also say that scoping of departments and has been fixed with the 9.62 update. I was unable to add them to scope in policy. For some reason in 9.61 they disappeared. Same with Departments. (Ops sorry if this was unrelated).

I can confirm here that updating to 9.62 solved this issue.