Abbylind,
We full-time in our 2009 BH-3670. Our furnace (since new) has intermittent indigestion as well. It seems to happen more frequently when the selected propane tank has run out and the auto-changeover regulator has actuated and the red indicator has popped up. This might suggest a propane pressure drop, as I understand that there is a reduction of capacity in this configuration. I have mud-dauber screens installed and have checked for obstructions etc. I also seem notice it more often after the furnace has been running for a few minutes. I have also thought that there may be an issue with condensation at the orifice, as damp combustion air passes through.
I haven't solved the issue, but it also has not caused any detectable problems. I also note that I have heard many neighbors furnaces making the same rumbling noises.
Sorry I can't offer any other insight, except that our rig does this too. Maybe someone else has experienced or fixed this annoyance and will share their remedy.