submodule/index/working tree woes

I have no changes to be committed (tracked or untracked according to
'git status') and yet when I try and switch branches git complains
that I have untracked working tree files that would be overridden
and aborts before the switch. 

The change I have just committed locally removes some files from the
repository and adds a submodule in it's place to better organize the
source for the project. 

Shaka, when the walls fell.  Anyone want to assist me with this issue?
Feeling clueless.