Try
Run %A_WorkingDir%\..\locationOf\script.cmd
Or
Run "%A_WorkingDir%\..\locationOf\script.cmd"
Or
Run %comspec% /k "%A_WorkingDir%\..\locationOf\script.cmd"
As BGM has said :
Keep in mind that the workingdir can also be changed via a windows launcher or shortcut. If you use a launcher like JetToolbar (my favourite) it sets the workingdir to its own application directory by default. It might be a good idea for the script to set the workingdir to the scriptdir or just use scriptdir instead.
Solution :
SetWorkingDir, %A_ScriptDir%