By referencing, yes.  I have it hardcoded in my ascx file.  I don't skin with html, only ascx.  The sequence is similar to what you say:

leftcontainer.ascx
skin.css

rightcontainer.ascx
skin.css

but these are in seperate folders and upload as seperate containers.  Originaly, the container classes were the same for both and I think this is what caused the problem.  One skin would affect all the containers even though all the containers had there own skin.css file.  I tried different naming schemes for the skins - skin.css, skin1.css, skin2.css, etc.  But all containers would be affected by changes to skin.css.  I overcame this by making each containers class unique and changing the skin classes to match the container classes.  My question is:
Is this DNN default or defunct?

Was there any resolution to this problem?  I woke up this morning to find that portal skins and container css files are no longer being emitted by dnn?

This was only happening on my production site and no updates occurred last night.  I'm on 4.3.5 (iis 6/2003 server) and using a purchased skin that's been working for the last couple months.  The skin and containers use external css and DNN has always pulled in the module/skin css files and added them to the head.  

I moved the db and code base down to a test machine and it worked fine.  Restarted IIS, killed the worker process..no good.  I eventually had to blow away the production directory and move my dev code base up to production and it worked. 

I've kept the various code bases for a massive diff but I don't think this will reveal anything as the code worked on my QA box.

Anyone have any further info on this? I really don't want to have another morning like this :)

Thank,
Bob
http://www.autisticvoice.com/bob