I'm not real sure I fully understand what the issue is but hopefully this might help.
Input using timecode is tricky from a processing level. Here's why:
When you play vinyl you want a nice signal level to reduce the impact of noise (signal/noise ratio). But the minute you back spin and start scratching the signal level shoots up RADICALLY. What happens is if you have a great signal during straight playback, it clips the phono preamp and does nasty things to control when you start manipulating the vinyl. Keep in mind, this is with vinyl time code, not CD.
If you've ever used an M-Audio Conectiv to record vinyl you'll notice the volume levels are really low. The hardware itself was designed to handle the control signal and peaks caused from vinyl manipulation. Some applications do this in hardware, others in software. Either way, the circles you have look good - so the signal level should work just fine on the input from the CV.
However, if I understand you correctly the OUTPUT from the mixer is too low. That would be driven by the output from the sound card and the set up on the mixer itself, and to a lesser extent from the software itself.
Except for rare circumstances, there really shouldn't be any reason to run the gains past 0dB (unity). It's all about proper gain structure throughout the signal chain.
And to keep this in mind... there are actually 2 signal chains.
Turntable->Sound card->Computer (STOP)
Computer->Sound card->Mixer->Processing->Amp->Speakers (Stop)
Even if the computer and sound card are shared between the two chains they are still separate.
I look forward to seeing the screen shots... I hope we can work to get this issue resolved for you.
