Never seen the issue you describe, probably cause I have two batch files which run (START and STOP) configured in PinballY and HideCursor=0.
I set the HideCursor=0 to help resolve issues I did see with the PC losing mouse control completely when the computer exited from the PinballY/VisualPinball.
Here are some of my settings ...
C:\myarcade\MousePlunger\mouseplunger.ini
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HideCursor=0
C:\myarcade\PinballY\Settings.txt
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RunAtStartup = C:\myarcade\MousePlunger\MousePlungerSTART.bat
RunAtExit = C:\myarcade\MousePlunger\MousePlungerSTOP.bat
MousePlungerSTART.bat
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@echo off
start /b /MIN C:\myarcade\MousePlunger\MousePlunger.exe
start /b /MIN C:\myarcade\visualpinball\PinVol.exe
start /b /MIN C:\myarcade\JoyToKey_en\JoyToKey.exe
MousePlungerSTOP.bat
--------------------------------
@echo off
taskkill /IM "MousePlunger.exe"
taskkill /IM "PinVol.exe"
taskkill /F /IM "JoyToKey.exe"