That is normal. The Buster r. 11 doesn't like being run at 16 MHz. In a
1997 usenet message, Dave Haynie explained it this way:
There have been reports of trouble with Rev 11 Buster in 16MHz A3000s.
This was supposedly tested and approved by PA at Commodore. But by
then, we weren't making 16MHz systems anymore, so there wasn't much
testing or simulation done in Engineering, if any, for the later
Buster revision.
It works when your PowerChanger 040 is installed because the Buster is then getting its clock signal from the accelerator card. It probably supplies a 25 MHz signal.