Someone on another forum recently had the same problem. Whether it's a new 'feature' of the booking system or a glitch, I don't know. The problem stems from the fact that the senior fare is discounted from the Value fare. As well known, as more tickets are sold, the fares increase. First, the Saver fare is gone. At some point...maybe 60-70% sold (I'm guessing), the Value fare is no longer available (and Senior discount), forcing prices to the next higher level. It's the same methodology Amtrak uses for sleeper accomodations and its various fare buckets.
It's quite likely there's a significant group of passengers traveling coach on the day(s) in question. Maybe a tour group or even a large group of gamblers heading for Reno. Although there's many coach seats on the train, if they're all or mostly sold out, even from Emeryville to Sacramento, for example, then there's little if any seats available EMY->CHI. Given that possibility, check if any Senior-priced tickets are quoted Reno->CHI and (DEN->CHI if none from Reno). If Reno shows Senior fares still available, then book two separate tickets...EMY->Reno at adult fare, then Senior fare Reno->CHI. There's absolutely no way CHI->NYP/NWK can be sold out. So book that as the 2nd part of a 'Multi-city' ticket (at senior rate).
Oh...and if you do the EMY-Reno(or DEN)-CHI booking, tell the conductor when boarding you're headed to Chicago (show him both tickets) so they direct you to the correct car. That way, you won't have to get off or change seats in Reno.
Although remote, it could also be possible that the computer hasn't been 'loaded' with the extended consists used during the summer, resulting in only 2 coaches, rather than 4 on the train, etc. Perhaps checking back in a week or so would give a better result.
Alternatively, if your travel dates are flexible, traveling on another date would likely have more seats available. Or, using the split at Reno as an example, book EMY-Reno the day before, spend a night in Reno, then travel to CHI from there on your desired day.