This turned out to be wrong constant in my code:
In one place PS3000A_DIGITAL_CHANNEL_0 was used, where PS3000A_DIGITAL_PORT0 should have been.
So bug in my code, and no problems with pico libraries.

Hi, I have 3406dmso, and I am using it with windows 10 and sdk. It is working fine in other ways, but when I 1) Configure no enabled analog channels, 2) Configure one digital port for capture I get error 0x10 from ps3000aGetTimebase2 call. If I configure both analog channel and digital port, it work...