Did you happen to notice the target's absolute altitude vice his differential altitude by changing the view option??  Am using the Navworx ADS600-EXP and the iPad.
Have noticed something very similar.  I show a discrepancy when displaying a traffic target's absolute altitude and then viewing the same traffic taget's differential altitude.  Then, using the altitude displayed on my altimeter, back-calculating the target altitude.  I show a 200-300 ft difference between the target absolute altiude and diferential altitude.
Wondering if IFly is using pressure altitude and not indicated altitude.  Anyone?