The AmigaOS 3.9 (including BB2 update) "AmigaOS ROM Update" doesn't work with the WarpEngine. It's probably the new exec.library in the "AmigaOS ROM Update". I haven't heard of anyone getting around this problem.
Ehmm, then I would be the first one I guess. My A4000 w/WarpEngine works fine with OS3.9 (can't remember which BoingBag version installed though). In fact it is the most stable machine I have ever used.
As for exec.library you can stop setpatch from loading it by adding SKIPROMMODULES "exec.library" to the setpatch line.