Maybe they are undergoing some maintenance....
Actually it might just be long lasting problem of the whole online ticket selling system. There are multiple reports about problems in general, problems with cards acceptance etc.. So you might simply consider purchasing ticket from DB. They don't sell tickets for Bologna-Salzburg or Linz, but you can buy ticket Bologna-Rosenheim/Freilassing (from 43 euro seats, 59 for 6 berth couchette) or Bologna-Passau (seats from 53 euro, couchette from 69 euro). Freilassing is basically outskirts of Salzburg, while Passau-Linz is rather short ride.
You can also hunt for OeBB discounted tickets, their online systems seems to work fine, but there are two conditions for tickets Italy-Austria bought from OeBB (only accepted in Italy if: "they have already been confirmed with a control stamp by a member of the ÖBB train crew on the jorney from Austria to Italy (I guess this will not work for you) or you have a member of the ÖBB train crew in the couchette coach or sleeper put a control stamp on your ticket immediately at the start of your jorney in Italy")
Not sure whether visit to Linz is essential for you or it is just a way to get to C.Krumlov? If it is the second option, then you might also consider buying ticket Bologna-Rosenheim from DB website, in the morning in Rosenheim purchase Bavaria-Ticket Single, visit Salzburg (the ticket is valid till it), then simply omit Austria and go to C.Krumlov via Bavaria (route via Plattling-Zelezna Ruda looks shorter, but via Wurh im Wald-Domazlice seems faster). You can also purchase Bavaria-Bohemia ticket instead, thus covering you Czech border-C.Krumlov part of the journey.
is the night train from Venice to Prague not running anymore?
Well, routes and schedules do change over time
Most of such overnight trains in the region run by CNL, more about up to date routes here
http://www.citynightline.ch/citynightline/view/en/index.shtml