Why is Git using the wrong ssh key

Putty does not store keys in an OpenSSH-compatible format. You need to use the "puttygen" tool to manipulate your private key.

(via this document, via Google):

To change or set a passphrase on an SSH key under PuTTY, do the following:

1. Run the puttygen.exe program.
2. Click on the "Load" button.
3. Select the private key file that you want to put a passphrase on.
4. Enter the new desired passphrase in the "Key passphrase" and "Confirm Passphrase" fields.
5. Click on the "Save private key" button. Overwrite the existing copy of your key.

Possible solution:

As I was typing the question I came up with a solution. But it seems to me there must be a simpler and more secure solution to this problem. What I did was change the value of 'command' in the authorized_keys file to:

command="~/somescript.sh" 

And 'somescript.sh' contains:

#!/bin/bash
ALLOW=(
    '/home/<user>/repository1.git'
    '/home/<user>/repository2.git'
)

case $SSH_ORIGINAL_COMMAND in
    "git-receive-pack"*|"git-upload-pack"*|"git-upload-archive"*)
        GITPATH=$(echo $SSH_ORIGINAL_COMMAND | sed -r "s:.*'([^']*)'.*:\1:g")
        ALLOWED="false"
        for ((i=0; i < ${#ALLOW[@]}; i++)); do
            if [ "${ALLOW[$i]}" == "$GITPATH" ]; then
                ALLOWED="true"; break;
            fi
        done

        if [ "$ALLOWED" == "true" ]; then
            eval "git-shell -c \"$SSH_ORIGINAL_COMMAND\""
        else
            echo "[ERROR] ACCESS DENIED" >&2
            exit 1
        fi
        ;;
    *)
        echo "[ERROR] Only git commands are allowed!" >&2
        exit 1
        ;;
esac

In the script I'm taking advantage of the fact that the commands git clone, git push and git pull produce on the REMOTE side:

git-upload-pack '<path>/<to>/<repository>', or
git-receive-pack '<path>/<to>/<repository>'

I specify repositories in variable ALLOW that are allowed to be accessed through the ssh key that uses the script, and simply compare them to the path specified in the issued git command (variable GITPATH). There is a security risk though, when multiple git commands are issued in one line. If the command contains at least one mention of an allowed repository, it executes the entire command. Any suggestions on improvement?