In addition to the possibility that your current custom footbeds are too bulky for those boots, there is also the possibility that if the footbeds are rigid, they're locking your feet into position and not allowing foot movement inside the boot, which is essential.
Here's a somewhat technical article that describes what needs to take place inside the boots and why semi-rigid footbeds work so well--
"Pronation is an important foot function and should be not eliminated, but controlled. Such early, unsuccessful experiments with [rigid] full arch support tended to discredit the general strategy. Now, the full arch support strategy has been revived using modern thermoplastic support materials. This allows for creation of custom supports with the proper blend of rigidity for control and flexibility for limited pronatory function and comfort."http://www.biomech.com/showArticle.j...leID=193000715