In some cases, clients aren't aware that they have a secondary (well, actually, primary) user-accessible quarantine that can be holding on to messages that don't appear in their spam/junkmail folder: one of my enterprise clients has this problem frequently (they use Postini). In other cases, the email is completely deleted by the client's mail server because it was considered too suspicious to risk later delivery.
Have you tried using Litmus, or a comparable tool, to estimate deliverability?
Do you have DKIM set up properly for your domain (while minor, any additional sign of legitimacy helps)? Also, check your bounced emails because the bounce reason may give you insight into why other messages are being silently disposed of.
These emails are showing a status of delivered, which leads to my confusion. DKIM has been verified in Marketo.
If they were receiving messages from an email client but are not receiving emails from Marketo- what else can I check on the Marketo side of things?
"Delivered" only means the recipient's mail server accepted them for (let's say, "as if for") delivery. It doesn't necessarily mean they even got close to a user's inbox.
You can send an email via Marketo to the Port25 tester at https://www.port25.com/support/authentication-center/email-verification/. Make sure to send to the email@example.com address.
Port25 can give you some vital insight -- or none at all. Unfortunately the rules that land a message in a quarantine can be (purposely) obscure, or even if they are not obscure they may not be surmountable. For example, we have some clients who simply don't care about their users receiving marketing emails (even if the users don't mind). They just dump everything that comes in via Marketo because (unluckily for us) they know that means the email is disposable.