As said before, your problem relies in the Amiga ROM Update file in Devs: folder.
The version installed with BoingBag 3.9-2 is incompatible with some hardware configs. I had a very simillar config, and had problems with this ROM Update.
Just look in the Devs folder, there should be an Amiga ROM Update.old or something (can´t look at my miggy right now), that´s the previous ROM Update. Probably the BB1 one. Just rename or delete the current ROM Update, and remove the .old (or anything like that) from the previous update filename.
Remember you have to power cycle your miggy to make the changes current, as the ROM Update is installed as a resident module.
Regards.