thanks for asking.

I too think this problem is caused by loading several apps at once at 
startup time. Doing this usually leads to concurring disk access 
which in turn leads to a massive slow down in disk performance for 
each reader (== programming loading). I had Safari and Mail launch at 
startup years ago until I got tired of the long loading times when 
compared to launching the apps sequentially by hand.

To answer your side question: there's no advantage in doing so. The 
feature was designed to help solve a problem with Apple® Remote 
locking at a time where I didn't know how to solve this problem much 
more efficiently ;-) .. I'll probably remove the feature again to 
avoid confusion and reduce possible error sources.

As for the long reaction time, I've no explaination other than that 
the system must be really busy at that time or AppleScript timing out 
while waiting for a response to an AppleEvent it sent to an application.

Best regards, 
Felix