Hi BOAC
Strange behaviour. I can't figure out a set of circumstances that would prevent programs loading, regardless of whether you are fleet of foot in logging in or tarry a while. I often log in as quickly as possible and have never experienced what you have.
This makes me wonder if there is a particular application that is misbehaving. Are you able to describe what's missing from your full house? Is it the same everytime?
There are several places where programs load during startup. I find msconfig and Hijackthis perfect for letting me see everything and control what loads. Generally speaking, the system registry and the startup program groups are where most things load. You already know the startup groups, the other places to inspect are;
HKEY_CURRENT_USER/Software/Microsoft/Windows/CurrentVersion/Run and it's equivalent key in HKEY_LOCAL_MACHINE.
The programs in these keys begin to load as soon as a user logs in. HKCU is loaded from a file in your user profile when you log on and is unique to each user. Don't be tempted to move programs from one to the other unless you are sure of what you are about. For example, a program loaded in HKCU can very reasonably assume that the current user registry "hive" is both loaded and unique to the logged in user. If that program where to load from HKLM and started before HKCU has finished loading, that would not be true and would likely result in tears.
You can run msconfig from the run box or a command prompt. Hijackthis is downloadable.
This article describes in some detail the entire startup process. If you find it too long or technical, I'm sure that googoo would find simpler explanations.
Troubleshooting the Startup Process
Hope this helps.
Regards
Simon