Git commands are not run from the correct directory on Windows

I installed Qt SDK 1.1.4, but only selected Qt Creator and documentation components (so that I can use Qt Creator to work on Qt 5).

This is a fresh install of everything. The machine previously did not have any development tools installed on it. After installing MSVC++ 2010 Express, ActivePerl, Git for Windows, and Qt Creator, I cloned https://git.gitorious.org/qt/qt5.git into C:\qt5 and only checked out the qtbase submodule:

C:\> git clone https://git.gitorious.org/qt/qt5.git
C:\> cd qt5
C:\qt5> git submodule --init update qtbase
C:\qt5> cd qtbase
C:\qt5\qtbase> git pull --ff-only origin master:master
C:\qt5\qtbase> git checkout master

I then built qtbase:

C:\qt5\qtbase> configure -opensource -developer-build -confirm-license && nmake

After building, I add this Qt build in the Build&Run configuration. I then load C:\qt5\qtbase\qtbase.pro into Qt Creator, importing the existing build, and start modifying some files. When I try to diff, the git diff command is run in C:\qt5 instead of C:\qt5\qtbase, so I do not see a diff of the files I've edited. When trying to commit, it shows C:\qt5 as the repository, not C:\qt5\qtbase:

From the Version Control output window:
09:08 Executing in C:\qt5: git diff --no-color --patience --ignore-space-change – qtbase

Diff shows:
diff --git a/qtbase b/qtbase
index 7dca461..c7730f8 160000
— a/qtbase
+++ b/qtbase
@@ -1 +1 @@
-Subproject commit 7dca461620ee6d8cce3a74acf2e1530d4497bff9
+Subproject commit c7730f8ec250eaeaa6f90ee5f86cfe06cbee4032-dirty