The registry loads in whole along with the selected user profile, the only difference is in Safe Mode, none of the startup entries (at any location) is initiated, also majority of the services are not started, only the bare minimum, system critical services are started (see screenshot).
So from what you have mentioned, the problem should be with either a startup entry and/or service(s). Your best bet is to use a program such as Autoruns which shows both, so you could disable (clear the box) the entries that you suspect. I'd suggest you click on Options and check the "Hide Microsoft Entries" option to be on the safe side.
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