Odd LF spike in Sound Card Calibration

After hearing about room calibration, I decided to give it a shot, but it seems I'm stuck on the sound card calibration part.

For reference, I have a UCA202 DAC/ADC as well as a Motherboard Line-in port.
The UCA202 mic input has a noise floor of -60dBFS, while the Mobo is lower, at -85dBFS which is why I want to use the motherboard line-in for calibration. Unfortunately, there seems to be some odd things happening.

Pictures are better than words, so here goes.
Here's sound out from the UCA202 going into line-in, at -12dBFS

Then Early tests of UCA202 out and UCA202 in, at -36dBFS (output peaks are -3dBFS)

And after repeating various combinations of USB out, in, motherboard out and in, getting pretty much copies of the top two graphs, the UCA202 in/out one mysteriously started working, giving this output.

I'm sure I can use the UCA202's ADC for a mic input (my home-made preamp has 0-60dB mic gain) but wouldn't it be more beneficial to figure out what's up with the motherboard sound input and get that higher-tolerance and lower-noise input option back?

Also, the mic I plan to use us a Behringer XM8500, and the factory supplied a lovely little calibration curve that I can use to equalize the mic; where would I be able to enter that manually in REW?

Regards,
Spring