I (think I) have a similar problem : I bought a MEGA1280, prototyping shield and ITDB02 + shield.
Photo of the proto board see http://www.ebay.com/itm/280747865279
Now, the proto shield moves the "horizontal" connectors down (it has separate header pins under and female headers above), and it has the pin headers under for the 2-row (pins 22-53) but no female headers, as they would not align correctly. So I can't connect the LCD shield at the same time...
Any suggestion welcome. My idea now is to replace the pins by "long female pass thru" so that it becomes transparent,
but then have to use pin 24 instead of 22 for D0, etc. Not even sure it would fit, as alignment is not perfect, like the infamous distance of PWM headers.
I hope this is comprehensible ?
For you, I understand you use a "short" ethernet shield between the mega and the ITDB02, so there is a gap between both for pins 22-53. I suggest you but "arduino female stackable shield headers" to connect your ITDB header with the mega. Ref at http://www.ebay.com/itm/180746311754