Just wanted to follow up with what I learned when I contacted Frontier.
The reason the flights wouldn't show up is that the layover is over 4 hours and according to them, their system will consider it an "invalid connection" if that's the case.
The schedule I had looked at involved arriving in Denver something like 1pm-2pm and leaving on the connecting flight at 8pm. Apparently Frontier's system considers this non-bookable. However they will book it over the phone if you call (and pay the extra fee for doing so, naturally... maybe I could ask them to waive it).
The reason why the return flight (OMA-SEA) of the itinerary was bookable is that it did not have a long connection time - more like 1h30m or 2h.
The confusion on my part was from the message on the website saying "Service is discontinued..." Really all that was happening is the flight schedules were changing to make it more difficult.
It would be nice if they'd let customers override this and choose their own connection. When I search for international flights on other sites, I get many ridiculously-low connection windows (such as 45m or 1h) available for booking, at airports it's very hard to get through in that time, with customs, layers of security, long gate travels, etc.
so it's very weird to me to have an airline say "Oh, you're staying in Denver for 6 hours until your next flight? Naaaah we can't let you do that!" I recall at least United would display connecting flights that were that long.
Oh well, I can't claim it makes sense but it is consistent at least.