Q: Why does my intel Mac Pro boot with multiple 'good' boot tones?

The following apple doc refers to multiple boot beeps

Power On Self-Test Beep Definition - Part 2

But what is confusing is your description about when the beeps occur, i.e, after the normal boot chime.  So that doc may be unrelated.

Try disconnecting all your periphials and see if the problem continues.

Try smc reset too.

See if it occurs if you boot in safe mode.

http://reviews.cnet.com/8301-13727_7-57383970-263/how-to-address-a-constant-rebo ot-loop-in-os-x/

Not your issue but goes into what can happen during boot process and follows with troubleshooting steps.