One thing i noticed while deploying SQL Express 08 is that it does not like using %~dp0 from within an install script, i had to revert to calling a UNC path from within the install script.
IE:
@echo off
\\<FileServer\SourceDirectory>\SQLEXPR_x64_ENU.exe /ACTION=INSTALL /FEATURES=SQLEngine /INSTANCENAME=EXAMPLE1 /SQLCOLLATION=Latin1_General_BIN /SQLSVCSTARTUPTYPE=Automatic /SQLSVCACCOUNT="NT AUTHORITY\SYSTEM" /SQLSYSADMINACCOUNTS="BUILTIN\ADMINISTRATORS" /IAcceptSQLServerLicenseTerms="True" /Q
exit
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