I use max 5 and the pandasoft exporter. ive never had a problem with different scales like that. i customized the grid settings in max so that if i make a box 10x10x10 (even multiple) when i import them into dbp they are actually 10x10x10.
ive never had a problem with two objects that are modeled the same size being different sizes in dbp. what version of the exporter are you using?
[edit] tried looking around the forums, i had posted a link to a website that had the configurations for pandasoft so that they worked perfect in dbp even with animations. if anyone knows that link or what the settings should be, i could use the info again as well!

P4 3.5 GHz HT, 1 GHz FSB, 1 GB PC4000, ATI Radeon 9800XT