I'm not 100% sure that the DOS software stores the carousel position...
If it did, then it will probably in the none-volotile memory of the Baldor control board (like it is now, on the modern machines)
So that would suggest the battery has also failed on the new board - I'd try replacing it again.
If you don't want to try that then maybe you can get into the habit of calling tool 1 before powering off everytime
