Hey Alex!
We (Us + Marketo Support) couldn't figure out why the blank template issue was happening (and they couldn't re-create the issue on their end to troubleshoot further). Fortunately, it only happened a couple of times, and then went away on its own... it happened shortly after we upgraded our Outlook plugin, so am not sure if it was just a delay in the upgrade working smoothly, taking a day to synch up and work correctly? (Not sure why that would be, so that's complete conjecture on my part... seems like it would work smoothly right off the bat!) That said, after the first few times, it hasn't happened since but, still unsure why it happened in the first place!
As for the MktUnknown situation... that's an interesting one! Seems to me, that if they're sending and tracking an email, to an address that is exactly the same as one that's already in the system, that MktUnknown lead shouldn't be created. But, maybe there's a connectivity issue or delay at the time of sending, that causes the system to not recognize the email temporarily (again, conjecture). Of course, while the email will still go out successfully, it just forces you to go in and merge those new records with the old ones, so you have all activity history attached to one common record. Sorry to hear that!
I bet if you log a Support ticket, they might be able to identify why that's occuring. Good catch!