Thanks for your persistence with this, I appreciate it!
I realised there's one obvious thing to try which I should have mentioned earlier, which is to try rebuilding your stack, and the System Stack (right-click in the stack list and choose "Rebuild...".
However, I do think I am seeing a potential cause; thanks for creating the super-minimal replication example. I noticed something in the nginx config override in there, which is that it contains the port numbers chosen by Indigo for the site when you ran it last. In Indigo's UI you've left the site config's port number choice on "Auto", which is a good choice, but it means that Indigo may choose a different port on each run. That means it's entirely possible Indigo will be getting confused about which port it expects to find the site on (which it needs in order to auto-configure the reverse proxy etc) vs what the site is actually (attempting to) run on (which will be what's hardcoded in your config override).
The chances of a port conflict in this scenario is high, exacerbated by the fact you have a large number of sites in the stack, and thus a lot of ports in use. It also would explain why the same site config runs fine on my Mac (I don't have the same ports in use that you do).
As easy way to sidestep this may be to choose a port (any arbitrary unused one is fine) in the site config, rather than using "Auto". However, the correct way to avoid it when overriding a config is to use the template config as the source, not the "compiled" config:
ie
- yours came from:
~/.indigo/stacks/AF1776/nginx_8899/conf/sites-enabled/test.test/conf
- correct source would be
~/.indigo/stacks/AF1776/nginx_8899/Indigo-template-src/templates/generic.php.conf
Using the latter allows Indigo free reign to apply your config from the UI etc as needed; using the former hardcodes these values which would cause problems if they change.
As a result of working this through with you I am realising more fully the extent of the UX issues around this system in Indigo, so I'm really appreciative of your patience and persistence. Your experiences will directly inform design decisions for improving the way Indigo handles config customisation.