If I use your open command, I won't be able to execute another perl command while $COUNTERS_NAME executes...

Not true, you can.

I have to "Wait" after $COUNTERS_NAME executes for one minute.

You can use sleep(60), or poll time, ...

Can I set STDOUT to go to a file before calling Win32::Process::Create(), then set it back when done?

I think you could execute cmd /c mycommand args > outputfile instead of just mycommand args