The issue is due to an internal CFHTTP call in the navserver.cfm that is hardcoded as "http". It never times out because there is no hardcoded timeout in that CFHTTP call and by default the ColdFusion Administrators timeout is disabled.
The TechNote below provides a hot fix for this issue:
ColdFusion MX 6.1: Hot Fix for ColdFusion Administrator Navigation Frame on an SSL Site