ThinApp do not hinder saving the password in anyway. ThinApp does not change the functionality of an application. What I suspect is that the location where the password is being cached is not being sandboxed. So ThinApp doesn't even touch it. The password is therefore stored somewhere outside the sandbox. Where and if possible to sandbox the location all depends on the application it self. I don't know Sametime and where it saves passwords.. Perhaps Nektra's Spystudio or Processmonitor can give you the answer.
In order to sandbox content please refer to this blog post on isolation modes: ThinApp Isolation Modes explained - VMware ThinApp Blog - VMware Blogs