What model TV do you have? What audio sources have you been testing the system with?

I have a samsung qe55qn95 tv connecting into the arc ultra via eArc.

Sources I've tried so far are the tv streaming apps and music streamed over WiFi to the system from my amazon.music account 

Be sure the TV is set to these settings:

HDMI-eARC Mode: Auto

Digital Output Audio Format: Pass-Through

Also be sure to perform Trueplay tuning and adjust the EQ settings, Height Audio, and Surround Audio levels to your liking.

Try to test the system with Dolby Atmos and 5.1 audio sources.

All set as you suggest apart from the digital output audio format.  I can only select auto or pcm.  I'm in auto.  In pcm it sounds dreadful.

I've tuned trueplay and toggling that doesn't really make a big difference.

Tested several multi channel sources including atmos. I can see the system recognising these formats in the sonos app so that seems to be working OK.  

I think what I'm a buit worried about is that is there an issue with my arc ultra. The suba and era 300s sound great but it's like there is something really missing from the front channels. Especially as I need to use 2/3 volume to get a reasonable output.

I rrealise this is not a particularly scientific comparison but the scale of the q990d that i heard tonight  (without rears hooked up) made me question if I have a a technical problem with my ultra

Make sure Night Sound is NOT enabled and the volume limit is set to 100% in the Sonos app.

Both those settings are as you suggest.