Hi,
hm, that's a weird problem.
Maybe you wanna check the asset-related tasks capistrano executes during the deploy:
link to source here. It's really simple to understand and maybe it will ring a bell for you.
Are you also upgrading Rails or Ruby version in this process? I don't know how capistrano could have anything to do with the output from "stylesheet_link_tag and javascript_include_tag helpers".
Question: why aren't you using 'capistrano/rbenv' gem (or capistrano/rvm if you prefer that)? I see it's commented out in your Capfile.
How do you even know which ruby/rails version your app uses on the server without that?
Not a really helpful answer, but maybe it generated new ideas for you.