Git rebase fails, 'Your local changes to the following files would be overwritten by merge'. No local changes?

Here is my transcript from trying to merge my bugfix branch onto my master branch in preparation to push it upstream. There have been some upstream changes pulled into master since the bugfix branch was created, and it now refuses to rebase.

The files it throws errors on are not diffed when opened. no files have been added, removed or renamed. Nothing is ignored and nothing is untracked or staged or unstaged. I'm completely stumped as to why the rebase is failing.

I'm on OS X 10.6.6 and git 1.7.4

.-(/Volumes/joshua/www/txfunds)-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------(joshua@Kusanagi)-
`--> git rebase bug586-test master-test
First, rewinding head to replay your work on top of it...
Applying: - comiitting code related to api permissions
Using index info to reconstruct a base tree...
Falling back to patching base and 3-way merge...
error: Your local changes to the following files would be overwritten by merge:
	inc/data.inc
	templates/apipermissions_tpl.inc
	templates/currencies_tpl.inc
Please, commit your changes or stash them before you can merge.
Aborting
Failed to merge in the changes.
Patch failed at 0001 - comiitting code related to api permissions

When you have resolved this problem run "git rebase --continue".
If you would prefer to skip this patch, instead run "git rebase --skip".
To restore the original branch and stop rebasing run "git rebase --abort".



.-(/Volumes/joshua/www/txfunds)-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------(joshua@Kusanagi)-
`--> git status
# Not currently on any branch.
nothing to commit (working directory clean)



.-(/Volumes/joshua/www/txfunds)-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------(joshua@Kusanagi)-
`--> git rebase --abort
HEAD is now at 5efccf1 - comiitting code related to api permissions



.-(/Volumes/joshua/www/txfunds)-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------(joshua@Kusanagi)-
`--> git log -n10 --oneline
5efccf1 - comiitting code related to api permissions
a8a5ee4 Style changes for IE
cfca618 Style changes for IE
8a69de6 Style changes for IE
8946585 - comiitting code related to api permissions - fixed an html error in the currencies template
5fba0a9 Merges the 1.11b branch bugfixes and changes into trunk
ef57049 Andrew Commiting on Blakes behalf on changes he made to transfers; Also an Indue GW balance fix; debitcarupload fix for LSN
69e4313 Fixed an issue with Support From email
9058fb6 Sets the svn property svn:eol-style to LF, to enforce unix style line endings
240839e Fixes up a lot of the whitespace issues.



.-(/Volumes/joshua/www/txfunds)-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------(joshua@Kusanagi)-
`--> git checkout bug586-test 
Switched to branch 'bug586-test'



.-(/Volumes/joshua/www/txfunds)-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------(joshua@Kusanagi)-
`--> git log -n10 --oneline  
b7b1f8a Resolves #586, Postback on deposit
5fba0a9 Merges the 1.11b branch bugfixes and changes into trunk
ef57049 Andrew Commiting on Blakes behalf on changes he made to transfers; Also an Indue GW balance fix; debitcarupload fix for LSN
69e4313 Fixed an issue with Support From email
9058fb6 Sets the svn property svn:eol-style to LF, to enforce unix style line endings
240839e Fixes up a lot of the whitespace issues.
cf27b6f - bug that came up with transferring. The transfer page had a hidden field called to, which was taking precedence over cards and usercard which would throw the system out a bit
7c21a81 Fixes #603, new add transaction form, journalled.
01e6292 Removes a pile of resource forks
880c5bc - bug that came up with transferring. The transfer page had a hidden field called to, which was taking precedence over cards and usercard which would throw the system out a bit



.-(/Volumes/joshua/www/txfunds)-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------(joshua@Kusanagi)-
`--> git rebase master-test bug586-test
First, rewinding head to replay your work on top of it...
Applying: Resolves #586, Postback on deposit
Using index info to reconstruct a base tree...
<stdin>:52: trailing whitespace.
				'name' => 'Invoice Transfer Out', 
<stdin>:175: trailing whitespace.
		
warning: 2 lines add whitespace errors.
Falling back to patching base and 3-way merge...
error: Your local changes to the following files would be overwritten by merge:
	templates/deposit_tpl.inc
Please, commit your changes or stash them before you can merge.
Aborting
Failed to merge in the changes.
Patch failed at 0001 Resolves #586, Postback on deposit

When you have resolved this problem run "git rebase --continue".
If you would prefer to skip this patch, instead run "git rebase --skip".
To restore the original branch and stop rebasing run "git rebase --abort".



.-(/Volumes/joshua/www/txfunds)-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------(joshua@Kusanagi)-
`--> git rebase --abort
HEAD is now at b7b1f8a Resolves #586, Postback on deposit

This is the same answer as another one of my questions re git troubles.

I'm on a mac, and this obscure config change seemed to fix all my woes regarding unstaged changes when there were none.

git config --global core.trustctime false

I think it's to do with differences between windows file times, linux file times and mac file times. who knows, feel free to comment if you do.

Update: This blog post explains what's going on, sort of.

With regards to Joshua Hogendorn's answer: it seems to me that leaving Xcode open while working on the repository with git leads to these problems. It even led to a situation where git committed something that I thought to have stashed (and still had afterwards) but Xcode just wrote to the filesystem right during the rebase.

So: Close your Xcode project before you work on the repo with git if you want to be safe, and then you probably don't need the core.trustctime false setting.