Whilst I canāt see the changes in your index.php you were referring to; it might have to do something with paths not properly setup. AFAIK you shouldnāt tamper with setting up the path to the assets folder by hand; thereās a helper for that.
My directories are set up as per the standard vanilla install of Kirby and the extra subs directory. The directories are as you would expect underneath (sites has templates, blueprints).
subs
subdomain01
siteA
assets
css
templates
content
media
site
@texnixe - I am only just starting to learn/piece together Kirby 3 and so as a designer I jumped to the CSS first.
The panel works without a problem for all subsites that I have created. The INDEX.PHP above is what I am currently working with just for test, but I had 8 subsites running with the panel at one stage.
It was when I then turned to doing a basic CSS for each of the sites that I ran into this problem.
Hm, Iām not sure that answers my question. What is in your assets/css/templates folder? Did you reference these files in your header using the @auto method?