Sounds slightly worrying. I thought bugs related to running stock OS was fixed by now. Any specifics on which events that trigger the bug(s) ?
They probably have, but I've never had a core update so I can't confirm anything until the new one has been released.
From memory, I had to disable several commodities that came installed as standard with OS9 and replace a couple of files with earlier versions. It was trial and error to find out what kept crashing the system. Finally, the last remaining big bug was that attempting to open the screen mode prefs would crash the system from Workbench. Not that I change my screen mode much, but it is bloody annoying. In order to change it I have to load the HDF file in WinUAE, change the mode, save it and then put the SD card back into the FPHA Arcade.
ClassicWB 3.1 works fine and the suggestion was that it was more likely to have been bugs in the softcore 68020. Again, I've never had a update to that core and I'm sure it is much better now.
Another bit of evidence that it was more likely the softcore CPU was that I'd get the same crashes on the Chameleon64 using the 68020 and OS3.9.
Oh, and one more: Jakub could run OS3.9 OK on his machine using a real 68060.