Curiously I seem to have fixed it without still knowing what happened.
I did a reset on globals on the HX (Holding FS4+FS5), intentionally I wanted to go though resetting things systematically to see what had an effect. The presets were the same. After the next boot:
1) Non-4CM patches Line out worked normally without need for patch leads looping the HX send/return
2) FX loop blocks suddenly became visible in the presets I couldn't get to work on the Helix floor! I was then able to disable them and Line out worked withitout need for patch loops. I then transferred them with the disabled presets into the Helix Floor, and again, magically the FX blocks were visible but disabled, so it could work as expected.
So whilst I "fixed" it with a globals reset, its a mystery how the FX block can be present but not display on screen or HX Edit, and how it can be enforced on all presets even ones which were never set up for 4CM. So if there are no hidden menu options to set this kind of behaviour (not sure why anyone would want it!), it seems like a bug.
Currently on latest FW and SW, but first saw this problem on FW 2.6