git rebase mixes commits
===

I have a very strange problem:
I have two separate branches and I am doing a simple `git rebase --onto branchA tagOnMaster`.
This is done via a script that used to work perfectly on my old 32 bit machine. Now I switched to a new 64 bit machine and it stops working correctly.  
It looks like git mixes commits.  
For example, I have two consecutive commits with the first commit changing files a and b and the second commit changing filec. Now, the rebase creates the first commit correctly, but the second commit contains the changes to file c and a **revert** of the changes in the first commit. This reverted changes however somehow are left behind in the disk and cause problems in the third commit.

I think some images will show better what happens:
 
First original commit which just changes a space:
![First original commit][1]

Second original commit which only adds two new files:
![Second original commit][2]


The first rebased commit - this one is correct:
![First rebased commit][3]

But now it is getting strange: The second rebased commit contains the reverse of the first rebased commit in addition to the two newly added files:
![Second rebased commit][4]

After that second commit the rebase failes to continue with this message:
> Database/Scripts/Versions/2.0.0/PKG_BODIES/normalinvoices.sql: needs update  
You must edit all merge conflicts and then
mark them as resolved using git add

And a look at the local changes reveals that the change from commit 1 is there again:
![unstaged changes][5]


I **really** would appreciate any insights into this.  
Is this a known bug? A *feature*?! Am I doing something wrong? Is it possible that the corporate anti-virus program somehow locks the files and thus messes everything up?  
And most importantly: How to get my rebase working again?

  [1]: http://i.stack.imgur.com/TLWfB.png
  [2]: http://i.stack.imgur.com/RjwdT.png
  [3]: http://i.stack.imgur.com/HktNR.png
  [4]: http://i.stack.imgur.com/fHl1m.png
  [5]: http://i.stack.imgur.com/1f5NY.png