Traveling on either Sept 18 or 19. Apparently I didn't find the discount prices when I searched DB Bahn.
What's your travel date? For 21 September I found discount fares as low as €29 on bahn.com and 763 CZK (currently €29.41) on cd.cz.
I just went to the German Rail (Bahn) website and input from: Praha hl. n. to: Berlin for Sept 18 at 9 AM. I immediately saw two Savings Fare EC connections at 10:29 and 12:29 for 29€/P ea. For Sept 19 the 10:29 connection was still 29€. The 12:29 29€ connections are apparently sold out; that price is now 39€.
For both 18 September and 19 September www.cd.cz is offering a fare of 763 CZK (€29.41) for every departure time all day long.
"www.cd.cz is offering a fare of 763 CZK (€29.41)" And that's probably the walkup price in the Czech Republic, no advance purchase required. Twice last (2012) May, I bought tickets from Czech Rail for a train ride between Germany and Prague. The ticket price (in Czech Koruna) was 1/3 to 1/2 of what the Bahn website was offering (in Euro).
My apologies for not replying to this sooner. I was able to purchase tickets through the Czech train website www.cd.cz An email sent to customer service gave me the assistance I needed to book. Final cost was $78.04 plus a small foreign transaction fee. Everything went smoothly with our travel and I appreciate those of you who took the time to answer my questions.