A most unusual problem has presented itself! I am connecting two batteries together (in series) and the voltage magically turns to around 2V...
My setup is as follows:
(http://matthew.kloiber.googlepages.com/problem.PNG)
It could very well be a problem with the batteries, but my multimeter is getting a constant 8-ish volts from each of them.
In case it helps, I am building an Ibanez FL-301 Flanger based off of the Tonepad layout. No part substitutions that I can recall. I will provide IC voltages if it would help diagnose the problem.
The obvious guess is that there's a miswire and it's dragging the voltage down. To prove it, unsolder the red wire from the power jack and then measure the series voltage with a multimeter.
Unwired, it measures the expected 16V. Would a faulty 12V linear regulator cause this problem? I had it in backwards before...
To answer my own question- just replaced it and it had no effect.
May as well go for the triple post!
It seems as if the protection diode may have died, it conducts electricity both ways. I believe I had a 1N4184 in there. Should it have been a 1N400X or a Zener?
Problem solved; thanks for your help, Aron. I'd like to think that without it, I wouldn't have known where to start. Those tricky diodes are out to get me.