I need to see your code.
I suspect, that you are creating your commands using Strings and than you probably do the
`...`
or the
Cmd(`...`)
wrong.
Please try to create a MWE which reproduces your issue without being overly complex. My guess is, while you do this you will solve your issue by your own 
MWE = minimal working example (Please read: make it easier to help you)
And I am pretty sure, that this creates an issue.
What is done with that is:
Julia exec a cmd.exe with ARGV[1]="start" and ARGV[2]="script.bat".
So cmd.exe will start interactive, runs start without parameter which fails. Now cmd as an interactive shell stalls whatever is expected to run now.
I think it would be best to just use
run(`PATH\TO\script.bat`)
without anything else. Or if this is not possible:
run(`cmd /C "start script.bat"`)
The " are important here, because
ARGV[1] must be /C and
ARGV[2] must be the whole āstart script.batā
You may be able to post again, thanx to @mbauman