What's odd is that only Band 2 seems to be having the unusual noise floor. It's normal to have a jump in the noise floor going to Band 2, but it's usually less than 10dB and I don't think I've ever seen such variation. Check against the specs as Bud suggests, but it doesn't look right to me.
Did you run the YTF calibration routine also? Note that this uses the COMB output and not the CAL output. I would also try re-running the regular self-cal after you've done the YTF cal.
There is a section in the Assembly-Level Repair Manual (see ref above from max-bit) that has some troubleshooting steps for this exact issue. See "If the analyzer displays a high noise floor" on page 234.
The noise floor appears high because during calibration the cal signal was low and the calibration routine increased the system gain to compensate. When you turn off the correction factors, those gain factors are removed.