It is caused by poorly written programs that run as admin and write to the registry each time they run. So you run the app 200 days a year and it creates 200 forks of the registry that need to launch in parallel at startup :-)
Um, the registry is an integral part of Windows. Lots of built in components read and write to it constantly. Fire up Process Monitor and you will quickly notice that there is lots of boilerplate registry accesses that go on that applications don't specifically perform (for example, if a program launches another program, Windows checks to see if there is an override in place for which application should actually be launched... in the registry). Registry access is a completely normal part of Windows, and is not a sign of a poorly written program.
I am also not sure where you get a write of the registry creates a fork. All I can think of is that there is the Previous Versions system which will back up previous versions of files, thus creating "forks". I am not sure if it is enabled for the registry (not sure how useful it would be, System Restore creates backups itself and Previous Versions is meant for user files) but even if it does only one copy would be loaded and actively used at once.
The only other thing you could be referring to AFAIK is Registry Virtualization. Legacy applications may have registry writes redirected for compatibility reasons (when NOT running as admin), but those go to a different location in the same registry; it doesn't create copies of the registry to store these redirected writes.
Of course as you create more registry cruft from installing more applications things COULD slow down in various ways unrelated to the performance of the registry. Most likely is you'll see Windows Explorer slow down as it interoperates with third-party components a great deal, and thus there is ample opportunity for broken components to cause delays or timeouts in things like right-click menus. The only thing the registry has to do with this is Explorer reads configurations on how to use third-party components from there. When people talk about "fixing the registry" it's usually in cleaning up the mess broken third-party components have left, and not any performance issues in the registry itself.