And this is what I get when I add those CR files to the Unsafe file list (which they will permanently be added). The references are in both runs...
Code:
; ********** Version 8.0  Build 0
; Randem Systems, Inc.
; Copyright 2003-2008
; Website:  http://www.***********
; Support:  http://www.***********/cgi-bin/discus/discus.cgi
; OS: Windows XP 5.1 build 2600 (Service Pack 2)

; Date: November 18, 2007

;              VB Runtime Files Folder:   E:\Server Data\Randem\Develop\**********\VB 6 Redist Files\
;     Visual Basic Project File (.vbp):   E:\Works\tibor\testcr.vbp
; Inno Setup Script Output File (.iss):   E:\Works\tibor\testcr Release.iss

; ------------------------
;        References
; ------------------------

; Visual Basic For Applications - (MSVBVM60.DLL)
; Standard OLE Types - (OLEPRO32.DLL)
; OLE Automation - (STDOLE2.TLB)
; Crystal Report Viewer Control - (crviewer.dll)
; Crystal Reports ActiveX Designer Run Time Library 10.0 - (craxdrt.dll)


; --------------------------
;        Components
; --------------------------



[Setup]
AppId=TestCR Release

;-----------------------------------------------------------------------------------------------------
; Taken from VBP Project File Parameters AppName, AppName AppVersion and Company
;-----------------------------------------------------------------------------------------------------

AppName=TestCR
AppVerName=TestCR 1.0.0
AppPublisher=

;-----------------------------------------------------------------------------------------------------

AppVersion=1.0.0
VersionInfoVersion=1.0.0
AllowNoIcons=no
DefaultGroupName=TestCR
DefaultDirName={pf}\TestCR
AppCopyright=
PrivilegesRequired=Admin
MinVersion=4.0,4.0
Compression=lzma
OutputBaseFilename=TestCR100Release

[Tasks]

[Files]
Source: e:\server data\randem\develop\**********\vb 6 redist files\msvbvm60.dll; DestDir: {sys}; Flags:  uninsneveruninstall regserver restartreplace sharedfile; OnlyBelowVersion: 0,6
Source: e:\server data\randem\develop\**********\vb 6 redist files\oleaut32.dll; DestDir: {sys}; Flags:  uninsneveruninstall restartreplace sharedfile; OnlyBelowVersion: 0,6
Source: e:\server data\randem\develop\**********\vb 6 redist files\olepro32.dll; DestDir: {sys}; Flags:  uninsneveruninstall regserver restartreplace sharedfile; OnlyBelowVersion: 0,6
Source: e:\server data\randem\develop\**********\vb 6 redist files\asycfilt.dll; DestDir: {sys}; Flags:  uninsneveruninstall restartreplace sharedfile; OnlyBelowVersion: 0,6
Source: e:\server data\randem\develop\**********\vb 6 redist files\stdole2.tlb; DestDir: {sys}; Flags:  uninsneveruninstall restartreplace sharedfile regtypelib; OnlyBelowVersion: 0,6
Source: e:\server data\randem\develop\**********\vb 6 redist files\comcat.dll; DestDir: {sys}; Flags:  uninsneveruninstall restartreplace sharedfile; OnlyBelowVersion: 0,6
Source: e:\server data\randem\develop\**********\vb 6 redist files\vb5db.dll; DestDir: {sys}; Flags:  uninsneveruninstall restartreplace sharedfile; OnlyBelowVersion: 0,6
Source: e:\works\tibor\testcr.exe; DestDir: {app}; Flags:  restartreplace sharedfile; 

[INI]
Filename: {app}\TestCR.url; Section: InternetShortcut; Key: URL; String: 

[Icons]
Name: {group}\TestCR; Filename: {app}\TestCR.exe; WorkingDir: {app}
Name: {group}\{cm:ProgramOnTheWeb, TestCR}; Filename: {app}\TestCR.url
Name: {group}\{cm:UninstallProgram, TestCR}; Filename: {uninstallexe}

[Run]
Filename: {app}\TestCR.exe; Description: {cm:LaunchProgram, TestCR}; Flags: nowait postinstall skipifsilent; WorkingDir: {app}

[UninstallDelete]
Type: files; Name: {app}\TestCR.url

[Registry]