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I loaded it once and power cycled it, couldn't see anything, so I reuploaded the firmware and tried both power cycle and the --reload. I also enabled the additional encoders in my hal file.

Did you power cycle the 7I76EU (or use the --reload command)?
 

Loaded up the firmware, but I'm not seeing the stepgen index-enable pins.  I looked in hal configuration and halcmd show pin in the terminal but I couldn't find them.  Would it make it easier if I picked up another 7i85S so I could have an encoder for each stepgen?  Thanks again for your help.  

Thanks so much. I really appreciate it. I'll load it up and give it a try.

I had assumed it was something I had wrong in my .py file. I'm not bothered by them if they are not really a problem.

OK the Linuxcnc image is Debian with a custom kernel.
The kernel has been configured for the Realtek 8169.
First things:should list the hardware and the driver that is loadedwill list all interfaces whether configured or notwill list any messages related to ethernet devices.
Just thinking aloud, it could be a firmware issue. The Realtek devices can be a bit of a PITA and usually, dont do this yet, a dkms package to suit needs to be installed otherwise latency can be an issue.
Just to let you know I'm connected to my RPi5 in the garage via wifi, the RPi5 is in the Waveshare metal case and surrounded by metal shelving
Once you have all this info please post to forum. Maybe be an idea to redirect the output of each command to a separate file, saves clogging up the forum and makes it easier to read and use grep.
I wouldn't recommend running a cnc machine via a remote connection....just saying.

It's a little odd because muxed cards are intended for encoders, so muxed encoders
and muxed stepgen index signals assume that there are an equal number of stepgens
and encoders. This could be fixed by adding a new pin type (muxed stepgen IDX)
but that would also require LinuxCNC driver changes, at least if done right.  

Here is an attempt:

 

I believe this has the stepgen index mapping the same as yours
for the first 6 indexes (0..5) , but then uses standard encoder pinout
for stepgen index 6 and 7 (since this allows 2 full encoders with shared
stepgen/encoder index pins) 

So you get 8 stepgen index pins, 3 working encoders (2 on the 7I85S and 1 on the 7I76EU)

A disadvantage of this current scheme will be that you need to enable all the encoders
even though only 3 are actually usable. I will take a look at better support for stepgen index
inputs using muxed cards, but as I mentioned, this will require LinuxCNC driver changes

I will take a look at fixing this but as I mentioned

Great!
Thanks for elaborating Hakan.
I did wonder about using DHCP when I saved these settings. Whether you use dhcp or manual it does not matter because you will not have a DHCP server on your ethercat segment so either way, you won't get an IP address. manual is probably a better choice.

However, in my testing, having an IP address is not an issue for ethercat (eg if your NIC is set up for a Mesa Card on 10.10.10.1)

ifconfig has been deprecated for a while (from Debian Bullseye from memory) so I would not recommend its use in a config file as its bound to bite down the track. In fact, I would be surprised if the command is installed in Trixie by default.  It wasn't in previous Debian versions.

Different operating systems may take a different approach to EEE so explicitly disabling it is a more defensive strategy than accepting the default. Be sure to check which driver you use.

The latency eliminating coalescing setting for Intel cards is mentioned in the Mesa hm2_eth documentation. type man hm2_eth to review. Ethercat is a more efficient protocol then hm2_eth so it may not be required but we do want a robust machine!

 

When you say it like that it seems perfectly logical ,
Still have the old cables for the two other axes so would need to have a look at them, thought I could find any useful information in the old drawings but came up blank.

Could the issue be bad connection to ground?
I did not check the resistance but pinged it direct to the chassis with a DMM and got connection, but did not look for how large resistance i have.