HnS does put in a top level bootloader, which hands control to BCD for Vista, or directly to NTLDR for XP (without going via the Vista BCD), but that boot loader takes as long as it takes you to make your selection, or as long as your default timeout if you don't chose.
Are you saying that it takes you 5 minutes to get past the boot menu choice, or that the whole windows startup is taking 5 minutes ?
The latter is a windows problem and, as Mak said, nothing to do with HnS, which is out of the process the moment the boot menu disappears.
Google for "speed up windows startup" or somesuch search, and you'll find loads of sites showing you how to identify and remove a lot of the startup bloat to speed up your system.
Remember, if you've just installed Vista, that it takes hours setting up its search indices when the system is new, and that slows things down a lot early on.
Well from what i have tried with HnS i have not had or seen this issue before. No one has reported any issues with the boot process taking longer. So Guru will have to take a look at this and see if he can figure it out.