script
└── rails

where rails script does something like File.expand_path('../../config/application', __FILE__) which produces

/home/christian/uri:classloader:/config/application

instead of

uri:classloader:/config/application

not going over the root "uri:classloader:/" works, like File.expand_path('../config/application', __FILE__) gives 'uri:classloader:/script/config/application' as expected.

loading the script/rails with classpath:script/rails is even more messed up:
/home/christian/uri:classloader:/classpath:script/config/application