There’s a lengthy explanation from Bungie here as to why Halo 3′s load times are increased by installing the game the an NXE-enabled 360′s hard drive.
For the time-pressed reader: the game caches maps to the HD whether it’s loading from the disc or the drive. Hence, if it’s running from the HD, it’s reading and writing from the same source. Which means it’s slower than if it’s running from the disc. That’s the main reason, anyway.
Got it? No? Read the full thing through the link, thicko.