Dean-
Reflections?
Since it seems to be happening with both sets of mics... perhaps the Preamp has something odd going on?
Have you tried the same mic arrangement with a different Pre/AD ?
Do you use the same cables with both mics? Perhaps (this is a real longshot here) a crystalized solder joint causing a diode-like effect? (it
can happen, but is super-rare with modern solder and good technique)
Try any other set of cables.
Can you duplicate this in a test environment?
Have you touched base with whoever modded the Pre, so that they can see the waveform?
Vanark-
I recently recorded a show which had a Meyer reinforcement system set with some form of limiting on it.
I noticed about two songs into the show that I could crank the levels to peak at -3db and never topped 0bd.
The limiting / compression was on the source, in this case.
My peaks could have been -3db or -20db, depending on where I set the levels.
If there was strong soft clipping at the source, it would shown at -3db or -20db, depending on where my levels where.
This idea applies to each stage of the input chain.
The mic's built-in amplifier, the Pre, the A/D, and any digital (ie.- DSP) processing could each limit peaks and the levels applied after would simply "contain" them at the level recorded.
Here's a way to determine if the source may have been MP3 or mini-disk, although that doesn't really apply to your case, since you have a pretty solid idea as to the lineage:
http://ca.geocities.com/dkleined@rogers.com/audio/compression/Spectral.htm No matter what, it doesn't sound bad.
Normalize volume to the level to a peak of -3db for louder playback and you are good to go!