I also found boingbag 2 did not apply itself either. I found it did not change the names on the
"AmigaOS ROM Update" file nor the "NSDPatch.cfg. They were still both with the BB3.9-2 extension and the sizes were different.
BB2 asks you during installation whether or not you want to update the ROM update. If you select "No", it does not install it as per your wish.