As suggested by Matteo, our squeezing measurement issue can be related to homodyne. The idea is to check the visibility of homodyne by using two PD of homodyne and compare them. To check the visibility, I used BAB and IRMCtra to make the beat note. For the BAB maximum transmission, the new PLL locking frequency I got today is 315MHz (without green).

For homodyne PD close to IRMC:

BAB is 500mV

LO is 1.835V

In this case, I found PD is saturated. So I put an OD 0.5 filter in front of IRMC. After this, LO becomes 644mV.

The beat note is shown in the attached figure 1. In this case, visibility is 90.37%

For homodyne PD far from IRMC(everything is the same apart from this PD):

BAB is 498mV

LO is 647mV

The beat note is shown in the attached figure 2. We could see that it is saturated. This is strange because this PD should have the same response with the other. Or we should not use this homodyne in this way because it is designed to use both PD at the same time. Anyway, we should investigate if this is a problem or not.