Likely not directly helpful, but I have a very specific problem that IS antenna related. I use a DX Engineering (DXE) Amplified Vertical for most of my suburban listening. At least once a week the DXE "becomes confused" and the noise floor drops from the normal minus 120 dB or so to about minus 135 dB. The issue does not seem to be related to the power supplied to the DXE Bias-T, rather, it appears to be the connection between the bias T and my ELAD ASA-42 (A&B testing suggests that the ASA-42 is not the problem). Rebooting the Bias-T and re-seating the antenna connectors generally solves the problem.
My point is: don't be too cavalier about assuming that the a powered antenna or your feed line is not the problem.
Also, take a look at the "ATT" box. On start-up, the noise floor is occasionally depressed and my S3 shows "ATT 6dB." I NEVER attenuate, so why this happens is likely buried somewhere in the S2 software. Selecting "ATT 0dB" fixes things.