Seems the core uses a wrong index in the disk load config string, which means the second drive with the new firmware. It was just ignored with the old. However when I fixed this, disk still didn't work. So I decided to update the whole 1541 code from Dar. Now it has read/write support! (but I didn't test writing). Also replaced the sd card emulation with a thin wrapper based on the code from MiSTer by Soreglig, so now the 1541 code speaks directly to the MiST IO-controller without any emulation layers.
Here's the source code change:https://github.com/mist-devel/mist-board/pull/57
Here are the binary releases:https://github.com/gyurco/mist-board/releases
Now there are separate PAL/NTSC relases, with included Kernal. The clock multiplexer used in the combined release made Quartus' job very hard (and the compile time was 3x as now). The core had (and still has) some problems with reset, so if it doesn't boot, just press the reset button again for about 3 seconds, or reload the core.