Well I spoke with Evan and thanks to his help I was mostly able to figure out what was going on.

The device count on the dashboard is only reporting devices that I have enabled for alerts. I swore it used to just show the count for all devices online/offline but maybe I am wrong.

Once specific site I still had reporting issues outside of this. Devices that are monitored with alerts weren't reporting properly but with a suggestion from Evan we found that hiding the device, then scanning and adding it back in fixed the issue. So I will have to go thru the list and hide all inactive, then add them back in and rename them and all should be well again. Why the hiccup on this one site idk, but at least we have a workaround.

Thanks for the support Evan! Always glad to see good support and someone who cares and is willing to lend a hand.