I thought I did respond, sorry. I just loaded it in A.09.33.12 and I don't see any problem at all. I also tried it on A.09.42.01. No problem at all. Maybe you could try downloading the file from this forum website and try opening it again, instead of using your local file.
I've got no good answer for you. I am using an N5242A, but I doubt that is the problem. I have seen some problems in the past with languange settings affecting the way files are read. I can only say that I read the file in just fine when I tried it last time. Curiously, I think I did see a problem the first time I read it, but I cannot repeat that issue.
Other ideas are: maybe it is something with the size of the file and all the comment lines in the file, which is unusual for an S2P file (comments are typically not inserted in the body of the S2P file, but at the beginning).
It cleaarly appears related to the end of the file, as though the last line is being read in and a new line is created with a frequency matching the last imaginary number. Leads me to believe something is reading in the numbers incorrectly in your case, but as I say, I can't reproduce it. maybe someone else can chime in.
No, I suspect that the gamma values are an attempt to deal with the fact that the S2P file does not allow input and output impedances to be different (a defect that is corrected in the proposed version 2, which no one uses yet). Those gamma values were really just comment lines, and are not used by any S2P file reader that I know.
From your display you have two issues: a short cycle ripple with a frequency pattern of about 125 MHz, and a long cycle ripple of a few GHz. The short cycle ripple is almost undoubtably due to cable length.
It could be a loose or unstable cable during the calibration. The other cause is poor residual source match and load response in the cal kit.
THe ripple pattern has a p-p of about 0.2 dB, indicating a combination of residual source match and raw load match of about -40 dB. If the raw load match is on the order of -15 dB, that means your residual source match plus load match together is on the order of -25 dB, not too spectactular.
You can look at the raw source and load match directly using the calset viewer.