Submodule changes are shown by source tree even if the option "ignore = all" is set to a submodule. This is incorrect behaviour and seems to be unsupported.
You can read about this git feature on th eofficial documentation here http://git-scm.com/docs/gitmodules.
You can see a config file example at stackoverflow here
http://stackoverflow.com/questions/3240881/git-can-i-suppress-listing-of-modified-content-dirty-submodule-entries-in-sta