Your problem is that your gemfile defines: bootstrap 2.3.2.2, and you are using syntax for bootstrap 3.0.0. Note that the specifier ~> has a special meaning, best shown by example: ~> 2.3.2.2 is identical to >= 2.3.2.2 and < 2.4 (more info here).
CSS overrides anything that was written "before" the latest lines, so when you add the link in your layout, the CSS for bootstrap 3.0.0 overrides anything in your assets pipeline. Everything that continues working in your web app was simply not changed between these versions, everything that stops working was changed.
You can get what you want by using the syntax from the boostrap 2.3.2 refences guide. You will find the default grid system under the scaffolding link.