The main problem is that the ENG hboot (or pre-GB hboots) doesn't recognize something in the hardware of the new phones. The end result is that the hboot runs at about 50x slower. It eventually gets booted, and once booted to an OS (either the main OS or the recovery OS) it runs fine since hboot has exited and passed control to the OS. So anytime hboot is in control, things crawl at a snail's pace.
Because the OS runs fine and hboot has exited, it is possible to overwrite the hboot partition from the booted OS. That's what you are doing in the instructions that I posted a few posts back. Once the correct hboot is installed, all is fine.
Did your handset ship with Gingerbread on it? HTC Firmware > 2.36.xxx.x?
If so there have been reports of newer hardware having issues with the older HBOOT (ENG S-OFF). This can be identified by very long boot up times 15-20+ minutes.