Genar-Hofoen,
May have found the problem by doing some digging; despite moving my Elite install (it's a Steam based one but I start via a shortcut to the launcher) to my primary hard drive (an SSD) after clearing some space on it, for whatever reason Steam kept the old folder structure including the logs folder on the secondary drive! I looked in both folders just to compare what log files should have been saved by each client and was like "hang about why am I seeing files from yesterday!"
So looks like CL may have been doing everything right, the user changed all the settings correctly to what you would expect them to be and then Elite and/or Steam have said "I don't want to do that". I will change the log path back to the old folder and take the Elite client outside for a good thrashing (once it's back up and running). So yes while it is Unexplained Phenomena it appears to be from FDev or Steam's side in terms of file handling!
Edit: And to further confuse issues it looks like the client was saving the log files in the "correct" location and then one day just went "nope I'm putting them in the old location again", oddly I have three netlog files from this morning where I've made attempts to see if the server is back up, one in the new location and two in the old location ... Software eh?
Edit 2: So, solved now, deleted the old Elite folder, ensured path in CL is the new location. Both logs being saved in "correct" location and CL picking current system. No idea why it was flipping between the two. Definitely a client/Steam issue not CL. Thank you Genar-Hofoen for your patience and Mungler for your thoughts too. Just need to add in the missing jumps somehow without doubling up on entries!