I found the issue with the floppy not writing/formatting.....the external drive (Gotek) is in a Power Computing housing, which has a couple of switches on it. One of the switches has an "Antivirus" feature which disables writing to the boot block of the disk. It must also prevent the same for the internal drive when selected. Flipped the switch and that parts all good now
Strange I've never had this situation with this drive before, but I don't use floppies to write to much at all!
Unless I get some feedback here, I'm still googling to try understand the tick, or more importantly hows its generated outside the power supply and what effect it has on each system component