(1610) Clients showing up as compliant but patches aren't installed

[shsysadm]

Many of my clients are showing compliant status when I'm trying to deploy Windows updates, both for Win 10 1607 and 1511 clients.

Attempting to deploy KB4013429 it appears to be compliant on the machines but if I manually go to "check for windows updates" the very same patch starts downloading from microsoft.

At first the machines present me with:

Failed to attach update to the automation wrapper, error = 0x87d00215    UpdatesDeploymentAgent    3/18/2017 12:57:22 PM    2440 (0x0988)
Failed to attach update to the automation wrapper, error = 0x87d00215    UpdatesDeploymentAgent    3/18/2017 12:57:22 PM    6544 (0x1990)

And then jump over to saying there's no updates needed to be downloaded.

Do I need to set custom severity options for these patches in order for them to apply or am I missing something? I've had this issue on a few machines during previous months but at most 5-10 machines, this time it's well over 400 machines acting up.

Any suggestions?