Hey Phil,
It could be that one of the tension rod casings is touching the platform, hence when you put a board under the pedal, the whole drum lifts up and the casing is no longer touching the platform. The resonant side of the drum should be HIGHER than the batter side. Of course, this will cause most beaters to not strike the head squarely. However, if you end up with a DW pedal (I have the 5002A Accelerator model - and you can have it when you pry it from my cold, dead hands!! ha ha) their beater is curved perpendicular to a standard beater, so the head angle is not an issue.
To put it another way, when your bass drum is set up, you should be able to slide, say, a piece of cardboard under the drum without anything (besides the spurs and pedal) getting in the way.
Or, it could be that I've totally misunderstood the problem you are having! If you could send a picture, that would help.