Thumping sound has developed in vertical loop

Have about 7 weeks on my new installation of a Portage and Main 250 Optimizer furnace. Heating 9000 sq ft plus basement.Love the unit... really something to view the blue hot burn in the bottom!! and absolutly no visable smoke coming out the stack. I ran 60' of logstor 1 1/4" pipe into the house, pump is at furnace, Grundfos cast iron UPS26-99FC 3 speed model. I built an "H" looking header system to be flexable in that I can run some flow thru a filter to keep return temp up, or bypass house all together if needed thru a 1" bypass. First in my loop is a water to air heat exchanger, then on to a sidearm heat exchanger on a hot water heater, then on to where I have another identical furnace in the attic to feed another water to air heat exchanger, after this furnace water passes back down to basement where I turn and go to return side of my "H" loop to return to furnace. this is all 1" Pex inside. I have developed what is best described as a "thumping sound" that comes every 12 -15 seconds from the down pipe on the return side of this attic furance. It is 30-32' vertical rise to this unit in piping system. I know it's from air or to me seems like my pump can't shove enough around fast enough to keep air out. System is "open" at stove to atmospere. I removed the check valve from pump... thought it would restrict flow.... I have tried a pump that pumps 125' of head to try and bleed any entraped air out of pipes/heat exchanger but to no avail. Anyone have an idea of what causes this and how to resolve getting rid of it? Thanks for any help. Been a pretty mild winter but have had a few cold weeks so far... oh... 128-132 deg F out of registers, and 165 deg F on hot water. Run furnace between 180-185 to keep desolved O2 out of system, PH 9.6 East Tennessee.

quite possible... It worked for 5 weeks without a sound.. pump runs continuously. It all started when I turned the pump to low, had designed to run on med, ran on high for a couple weeks and was playing with system... think the long haul up was a strain on low but I thought when a system was "solid" what comes down helps pull up on the up side.. your theory makes sense. I'll try to lower overall temp down to 175-180 and see if thumping changes times per minute. I like an idiot put an automatic air bleed up there thinking that would let out any air...wrong... only let in more and system got air blocked completely... capped little bleed off tight and hooked up big pump into system and pumped air out. I'm thinking maybe my big pump I hook into my "H" header and valve in has developed seal leakage and may be putting air into the system somehow? I'll pick up another pump capable of exceeding that highth and good flow and see if that helps if lowering temp in stove does not. thanks.

Thanks...I'll ck that out! Temperature drop has lengthed the thumps and greatly reduced the "impact" of the problem ... not as severe now. The auto air vent, (remember this is open system at stove) only let in lots of air to the point it dried the pipe from the top over on the down side and eventially I wasn't getting flow for about an hour...only pumping dead headed. Thumps are spaced about 30-45 seconds apart and are light in impact nature now.... only change was dropping temp range from 180=185 cycles to 170-175... still wanting to run the higher numbers. Will a pump at the bottom of the loop going up help? ck valve or no ck valve???