Can having two expansion tanks above a boiler cause it to over pressurize?
Not sure why there would be two expansion tanks installed, I would look into that further.

To answer your question, yes expansion tanks can become waterlogged. There a two main types of expansion tanks, bladder and diaphragm:


  In a bladder tank, there is a rubber bladder that expands and
  contracts as fluid expands and contracts within the system.  In
  bladder tanks, there is no direct contact between the air in the tank
  and the fluid in the bladder which will reduce corrosion compared to a
  atmospheric tank.  Bladder tanks can typically fill 100% with fluid,
  reducing the size of tank needed.  The bladder is typically removable
  and/or replaceable allowing for simpler and less expensive repairs or
  inspections.  Bladder tanks also have an ASME option available.  They
  can also be floor mounted in the vertical position which can save
  valuable space.  Bladder tanks can also be purchased with FDA approved
  Butyl bladders allowing for use in potable water systems.  However,
  bladder tank usually have a higher initial cost and have a lower
  maximum allowable temperature than plain steel tanks because of the
  material of the bladder.
  
  In a diaphragm tank, there is a diaphragm that separates the fluid in
  the top of the tank and the air in the bottom of the tank.  Diaphragm
  tanks are similar to bladder tanks in that there is no direct contact
  between the fluid and air in the system, which reduces corrosion. 
  Diaphragm tanks require less maintenance and have a lower installation
  cost.  They can be floor mounted in the vertical position to save
  space and also come with an ASME option.  Unlike bladder tanks,
  diaphragm tanks have a limited acceptance volume, requiring a larger
  tank.  The diaphragm is not replaceable and the diaphragm tank has a
  lower maximum temperature than the plain steel tank because of the
  material of the diaphragm. Source.


I find that diaphragm tanks are more common now and I would guess that your newer tank is this type. Diaphragm tanks come pre-charged with air (depending on where is is installed this pre-charge may need to be adjusted). Over time, the tank may lose this air charge and need to be re charged.

Here's some information from about.com regarding this issue and how to fix it:


  Symptoms
  
  
  Pressure relief valve on boiler is spurting water
  Expansion tank is hot to the touch lower than the middle of the tank
  
  
  Possible Causes
  
  
  Too little air and too much water in the expansion tank
  
  
  Possible Repairs
  
  
  Turn off boiler, close water shutoff valve and let tank and system
  cool.
  Water-side pressure must be at 0 psi in order to get an accurate
  read of the air pressure on the diaphragm.
  Check the pressure in the
  expansion tank by attaching a tire gage to the air recharge valve
  (Schrader valve) at the bottom of the tank;
  If air is needed, add more
  by using a bicycle tire pump to fill the valve to 12 psi or as
  otherwise indicated by manufacturer's instructions.
  Open water supply valves and let system fill back up.
  Turn boiler back on (do this after water supply is back on)
  System will recharge. Let run for 1-2 hours and recheck.