When I do a search for new fares for a train I usually do about 30 searches on different days at one sitting, then wait until Arrow allows more searches. Prompted by your post, I just completed the search for both Silvers and both Lake Shores and only needed to make estimates for two fares not found.
So there's no glitch - just a simple fare increase. Increases in mid-bucket Roomette fares are 46% for the LSL to BOS, 21% for the LSL to NYP and a paltry 8% for the Silvers. Increases in the accommodation charge for the LSL are 14 & 15 % and 22% for the Silvers.
BTW, the only coach fare I bother with nowadays is the one charged for an additional adult in a Roomette (the one followed by the > symbol on the bucket chart). This "accommodation" fare is usually around middle bucket for a Roomette. Accommodation charges for Bedrooms and Family Rooms are higher.
And just in case nobody's noticed, Crescent fares have also risen.