Any chance the 9v battery in the STC-9000 is depleted? That would affect headroom and could cause clipping.
^ This is what happened... Unfortunately I was too slow to take your advice and it caught up with me over the weekend. I was stack taping 10' back and became aware of the problem when I needed to add the 10+ gain and the levels did not change. The levels were just too low. Luckily I successfully ran the rest of the show with the mics directly into a DR-05 with PIP. The part of the show recorded with the pre has each of the first few songs becoming quieter and quieter in Audacity. While I have not yet tried it with a new battery, I am sure this is what happened based on the evidence. Lesson learned - If in doubt, just change the damn batteries! It's only a few bucks and will save you from the frustration...
I can't vouch for Chris here, but I do know that with some preamps and recorders that run on AA/AAA/9Vs it is recommended to remove the batteries when not in use. Many electronics still pull a small current which over time can drain the battery or at the very least could negatively impact performance in the field. Not to mention you could get battery acid on your gear.