The folks at smallbizserver.net released an article explaining How to create a new website in SharePoint that is not accurate… and will potentially lead to problems (I tried to notify the author, but here is no contact ability on their website).
The article says you need to bind an IP to a SharePoint virtual server. This is not a supported configuration as outlined by MSKB #830342 . If you run an IP-Bound solution, you can experience errors locking out changes of a web part and loading tons of errors on the event log… specifically you’ll see “Error: Failure in loading assembly: AssemblyName”.
This obviously causes a issue when you want to host multiple SSL enabled WSS/SPS sites on a single server as you must either run in an unsupported configuration OR run every SSL enabled site above and beyond the first one because you can not use host headers in SSL.
I have personally confirmed this to be a limitation of WSS via a recent PSS ticket I opened with their level 2 support. Microsoft is well aware of the situation.