Error 128 Clone succeeded, but checkout failed

I have looked for an answer to the Error 128 Clone succeeded, but checkout failed message we are getting on a clone command. And there does not seem to be any that relates to our situation.

The repository is on a local file server system that is mounted to the pc as L:

If we clone the repository on to the L: directory structure we get the following

git.exe clone      --progress -v  L:\GIT_REPOSITORY L:\warrend\fail

Cloning into L:\warrend\fail
Done.
Fatal: unable to read "Long hash key"
Warning: clone succeeded, but checkout failed.
You can inspect what was checked out with git status
And retry the checkout with git checkout -f HEAD

Git did not exit cleanly (exit code 128) ( time and date etc)

At this point there is only a .git directory at the destination

We have another drive mounted as X: which utilizes a different file server. If we do this

git.exe clone      --progress -v  L:\GIT_REPOSITORY X:\warrend\works

It will clone and do the checkout properly.

These does not seem to be any permission or disk space problems on the L: drive. We are unable to figure out why this is happening.

I copied the two .git directories to a linux file system and did a diff -r of them and found this

Bad one doesn't have the putty line for some reason diff -r fail/.git/config works/.git/config 12d11 < puttykeyfile =

There was no index file in the bad tree. The config file which is in both trees was made after the index file. Only in .git: index

I was hoping there was a debug method that would allow us to see what the actual check was that is failing. Any help on this would be greatly appreciated.