In the thread linked below, it ended up just being bad sound ROMs that needed replaced on a Sega Independence Day pinball machine, it would be nice if were an easy fix like that in your case.

https://pinside.com/pinball/forum/topic/sternsega-independence-day-audio-issues

And from PinWiki:

http://www.pinwiki.com/wiki/index.php?title=Sega/Stern_White_Star_Repair#Sound_problems

Pages 34/37

Sound is distorted

If the sound is distorted, the most likely problem is the TDA1543 (U26) chip. This sounds as if the volume is very over modulated and are “clipped”. Be sure to use the TDA1543 version and NOT the TDA1543A. The TDA1543A uses another protocol (Japanese). If the sound is distorted at master volume levels below 4, see the section below that explains a fix.

Loud hum/burnt speakers/12V DC coming out of the speaker connector

If you have a machine with all speakers dead, check for voltage on the speaker wires. If the ­12V wire from the driver board to the CPU board is disconnected, it can cause 12V DC to be sent down the speaker line, causing a loud hum and fairly quickly destroying any speakers connected!

Loud Hum and / or Distortion at Low Sound Levels

Stern released Service Bulletin 133 (http://www.sternpinball.com/downloads/sb133.pdf) , which discusses a fix for a loud hum and / or distortion when the master volume is set below level 4. The machines that are specifically effected are Monopoly and Austin Powers. However, it has been over 10 years since these games have been released, and boards get transplanted to other games over time. So, it is important to check the two resistors (R106 and R110) in the amplification section of the CPU / sound board to see if the correct values are installed, regardless of the game. The correct resistor values should be 33K ohms 1/4 watt for R110 (ORG­ORG­ORG­GOLD), and 10K ohms 1/4 watt for R106 (BRN­BLK­ORG­GOLD). Consult the service bulletin for more details, and the layout of the amp section. The R106 and R110 control the analog volume. When these resistors are broken (open) the analog volume goes to 100% and can't be controlled via the buttons (digital volume) on the coin door. The higher the resistor value the higher the volume.

Good luck, keep us posted.

Perhaps those who do experience it are because of a bad EPROM or sound ROM? I'm really not sure what to think, but I really don't notice any of this and never have on any of the sound clips in my game at all.

Not disagreeing with you one bit here, either... It's definitely a mystery to me though, at this point.

Has anyone played The X-Files on Virtual Pinball? I'm curious if the sound is off there as well.

And of course, if any other owners of the real X-Files pinball machine have an example with good sound, it would be interesting to note. I can't be the only one without issues. I'm an audio freak too, I love high fidelity, sound quality and clarity.

Sweet, glad there's others with good sound quality on their X-Files. So I'm still leaning towards corrupted sound ROM chips and possibly a RAM issue being the culprit for the ones that do seem to have lesser quality.