You could try using "sc" instead of "net start"; it also allows you to set services temporarily to manual with e.g.:
sc config "Blackberry Server Alert" start= demand
and likewise "auto" and "disabled". You'll still need to quote the service name of course.
One thing to watch out for - if you have different mail servers (e.g. Exchange and Lotus) or different BES versions (e.g. 4.0 and 4.1) you might get slightly different service names. You won't get an "MdsTomcat" unless you've installed MDS Services, for example.
What do the logs say about the services not starting at boot though?
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