Reservations to Poland can generally be bought 60 days in advance and currently, it seems only until the end of the winter timetable (11 June). So you're indeed to early.
In addition, it's better to buy this reservation via Czech railways. Interrail wants 6€ plus 9€ for the privilege of sending it by post, while Czech railways charge CZK 75 (~3€) and send the reservation via e-mail.
Czech railways main website seems to be unreachable currently (they suffered a hacker attack - maybe that's still the reason) but their mobile website seems to work (also on a pc).
Krakow to Berlin is difficult to get online. I'd ask in Munich or Prague at the ticket office. A few days in advance should normally be OK.
Best is always to arrange it IN the country where train departs from-and other as all newbees here tend to think, these trains are NOT ´full.. monthes/weeks ahead-mostly hardly ever. Very much like in IE on IR. The trick we used in the past-when it was all paper and no apps etc: on arrival just spend an extra hr or 2 at arr station-go to desks, see how it all works (in that past the tourist office would book rooms-also before this www) and pay for the next leg. Is it really now that diffcult to think of by yourself?
AFAIK there are NO direct trains Kr (very nice town, also quite touristy) to B, you change in Poznan or maybe Wroclaw-the PL legs are ´free´ when done IN PL at counter, the train to B over the border is not but its like 4-5€-OR you can use other local trains=change more, takes longer.
BTW; CD=CZ rails also offers cheap advance tix Pr→ Krk for 19€ and there is also LEO express, a private company often even cheaper (mostly weekends),
AFAIK there are NO direct trains Kr (very nice town, also quite touristy) to B,
If you check the timetable, you will find that there is.