While upgrading ColdFusion from 9.0.0 to 9.0.1 we encountered an issue with ColdBox where the CFAJAXPROXY wouldn’t work any more (WDDX Error 500). To resolve this issue copy the CFIDE which was upgraded in /opt/jrun4/servers/cfusion/cfusion.ear/cfusion.war into each of your applications (where ever the mapping references).
It appears that the issue is caused by ColdBox loading the old version of the CFIDE.