I never tried
But simply changing
[Events]
OnNewDir = %EXEC ..\scripts\esmNewdir\run.bat OnNewDir %[$user]
into
[FTP_Pre-Command_Events]
stor = %EXEC ..\scripts\esmNewdir\run.bat OnNewDir %[$user]
might work... or maybe not, depending if ioftpd gives the same parameters to "OnNewDir" and to "stor".