I think I encounter another error that I did not realize. The SQL Server native client 2012 is not supported in XP, so the error message was ambiguous.
At least the IsWin64 directive is now working.

>Why don't you use IsWin64 directly?
>
>>I thought so too, first i tried
>>

>>function IsX64: Boolean;
>>begin
>>  Result := IsWin64;
>>end;
>>

>>But same result. perhaps it is not supported on VM, I am running a 32bit Windows XP VM and there it returns True.
>>
>>>You should check Windows not hardware http://www.jrsoftware.org/ishelp/index.php?topic=isxfunc_iswin64
>>>
>>>>Using innosetup for the setup procedure, I need to run a file after setup, depending on 32bit or 64 bit OS. I
>>>tried a few flags to check if the OS is 64 bit, but Innosetup seems to ignore those:
>>>>

>>>>[Code]
>>>>function IsX64: Boolean;
>>>>begin
>>>>  Result := (ProcessorArchitecture = paX64);
>>>>end;
>>>>
>>>>[Files]
>>>>; MsSql client:
>>>>Source: "..\Resources\SQLRuntimeFiles\sqlncli.msi"; DestDir: "{tmp}"; Components: CompleteClient; Check: not IsX64
>>>>Source: "..\Resources\SQLRuntimeFiles\sqlncli_x64.msi"; DestDir: "{tmp}"; DestName: "sqlncli.msi"; Components: CompleteClient; Check: IsX64
>>>>
>>>>[Run]
>>>>Filename: {sys}\msiexec.exe; Parameters: /i {tmp}\sqlncli.msi; WorkingDir: {tmp}; StatusMsg: Installing SQL Server Native Client Drivers.; Flags: runascurrentuser;
>>>>

>>>>It looks like it ignores the check and always copies both files. So when running the resulting setup.exe on a 32bit OS it gives the error message that it is not supported. What am I missing here?