I don't know if I buy the theory (put about in a thread on HydrogenAudio a couple of years back) that the developers were forced to use low-bitrate sound effects due to system restrictions, and therefore surreptitiously slipped pre-emphasis flags into the CD so the rolled-off treble would match the in-game sound effects better. It's more likely that the developers had nothing to do with the use (intentional or not) of pre-emphasis. I remember reading that Reznor insisted id Software provide the soundtrack in uncompressed CD audio as a condition of his participation, but I really doubt they had the budget to go to a fully-fledged music mastering house and pay a top-dollar engineer who knew what they were doing each time they patched/updated the software and had to assemble new master disks as a result. I'm leaning towards the pre-emphasis flags being set to "on" in some pressings (including mine) by mistake, and accurately set to "off" in others; it'd just be the result of when and where they assembled the master disk someone pushed the incorrect button.