Here's one way that can happen.
If you click in the margin to set a breakpoint on say line 3 in your DriveBackup.cmd file. Then save the file. Then close the file. The Debugger will save your breakpoints in a file named DriveBackup.cmd.bp so that when you reopen the file in the debugger they will still be there.
If you subsequently edit the DriveBackup.cmd file outside of the debugger, and add or delete lines, then when you reopen that file in the debugger the breakpoints will appear to have shifted to a different line. In reality they are on the same line number as when you set them, but the debugger has no way of knowing you changed the file.
Could this be your situation?