Windows – Non-domain joined clients unable to query DNS

This behavior is expected given your configuration. You shouldn't have the router's IP set as the secondary DNS for PCs and member servers or they'll always sometimes go there which you don't want. They should only have domain controllers as their DNS so all of their DNS traffic routes through the domain controller. You can then either configure your domain controller to forward to an upstream DNS server for domains it can't resolve (usually this would be your ISP) or just leave it alone and it will use the root hints servers to resolve external queries.

Typically you would want two DNS servers on the PCs and member servers and you would get that by having a second domain controller so DNS (and Active Directory) continue to function if the primary goes down.

This is NXDOMAIN hijacking, revealing to you a harmless aspect of how DNS search suffixes work.

I'm going to guess that your DNS resolution is to a local device, which contains copies of your zones, then does recursive lookups for other zones off of an internet server (which is doing NXDOMAIN hijacking).

A client with a DNS search suffix will issue additional queries with the chunks of the suffix appended. If my system has a suffix list of, for instance, foo.domain.com then domain.com, and I do a lookup against a single-name host server, it'll execute the following queries, in order, until it finds something:

server.
server.foo.domain.com.
server.domain.com.

(the . at the end is to specify, in DNS terms, that it's relative to the root and nothing else)

Which is great, and makes perfect sense. If server doesn't exist at server., it'll be looked for at server.foo.domain.com. - if it doesn't exist, it keeps going; if it finds an answer, it'll stop.

Where it starts to look a little less normal is when you search for something that you're thinking is the FQDN - but DNS doesn't know that (unless you're doing an nslookup with the . at the end). So, if I search for server2.domain.com, it'll search like this:

server2.domain.com.
server2.domain.com.foo.domain.com.
server2.domain.com.domain.com.

Those last 2 make very little sense to you and me, but the resolver doesn't know any better, and needs to check.

Which brings us to what you're seeing. Your search suffix list probably looks something like this:

domain.parentdomain1.parentdomain2.net
parentdomain1.parentdomain2.net
parentdomain2.net

And, your recursive DNS servers probably contain a zone for parentdomain1.parentdomain2.net, but not for parentdomain2.net.

So, the query happens like this:

hostname.domain.parentdomain1.parentdomain2.net.

(NXDOMAIN response - you'll want to look into why that is happening if this is where this record is supposed to be)

hostname.domain.parentdomain1.parentdomain2.net.domain.parentdomain1.parentdomain2.net.

(Your name server likely has a zone for parentdomain1.parentdomain2.net, and throws another NXDOMAIN)

hostname.domain.parentdomain1.parentdomain2.net.parentdomain1.parentdomain2.net.

(same result as previous)

hostname.domain.parentdomain1.parentdomain2.net.parentdomain2.net.

(Now, your DNS server forwards the query to your upstream forwarders for lack of an authoritative zone. Your upstreams dutifully send back a false response, in a misguided attempt at getting some extra advertising revenue)

So! This is likely a simple issue with a record, which got a lot more confusion because of abusive practices by your ISP or whoever else runs that upstream DNS server. There's a lot of variables that I've made assumptions on above, but do some checking on how things are resolving for specific queries (with . on the end to eliminate the search suffix) and it should track pretty closely with how I've outlined it.