Another thing to watch out for with Startup Scripts is the default timeout. Can't remember what it is OTTOMH but Windows will not wait forever for scripts to complete (Startup or Logon). The timeout can be set with GP.
In my experience, the problem with using IE for forms (apart from the ickiness factor) is that the user can easily close the IE form at which point if the script references it, it errors out.
Very good point by default it times out in 10 mins, i may have to re-think this one.