This problem applies only to Vista 64-bit systems.
V1.9.0.526 of PT 2009 does not display the startup entries correctly in Vista 64-bit. It fails to display HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run items. Because PT 2009 is apparently addressing the registry as a 32-bit registry, it does not properly see HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run and HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Run
I have other programs on my system that DO properly display the RUN keys....Ace Utilities, Vista Manager, AutoRuns and others. Below are the RUN registry keys on my system as addressed using the default 64-bit Regedit on Vista 64-bit. Also shown is the Ace Utilities Startup Manager and the PT 2009 Startup Manager.
Key Name: HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
Class Name: <NO CLASS>
Last Write Time: 2/2/2009 - 11 PM
Value 0
Name: PowerChute
Type: REG_SZ
Data: "C:\Program Files (x86)\APC\APC PowerChute Personal Edition\Display.exe"
Value 1
Name: IAAnotif
Type: REG_SZ
Data: "C:\Program Files (x86)\Intel\Intel Matrix Storage Manager\iaanotif.exe"
Value 2
Name: NvCplDaemon
Type: REG_SZ
Data: RUNDLL32.EXE C:\Windows\system32\NvCpl.dll,NvStartup
Key Name: HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Run
Class Name: <NO CLASS>
Last Write Time: 2/2/2009 - 11 PM
Value 0
Name: avgnt
Type: REG_SZ
Data: "C:\Program Files (x86)\Avira\Avira Premium Security Suite\avgnt.exe" /min /nosplash
Value 1
Name: THGuard
Type: REG_SZ
Data: "C:\Program Files (x86)\TrojanHunter 5.0\THGuard.exe"
Value 2
Name: UltraMon
Type: REG_SZ
Data: "C:\Program Files\UltraMon\UltraMon.exe"
Key Name: HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run
Class Name: <NO CLASS>
Last Write Time: 1/29/2009 - 8 AM
Value 0
Name: AutoSizer
Type: REG_SZ
Data: "C:\Program Files (x86)\AutoSizer\AutoSizer.exe"
Value 1
Name: Sidebar
Type: REG_SZ
Data: C:\Program Files\Windows Sidebar\sidebar.exe /autoRun
Value 2
Name: HostsServer
Type: REG_SZ
Data: "C:\Program Files (x86)\HostsMan\hostssrv.exe" --start
Value 3
Name: SUPERAntiSpyware
Type: REG_SZ
Data: C:\Program Files (x86)\SUPERAntiSpyware\SUPERAntiSpyware.exe
Value 4
Name: WeatherWatcherLive
Type: REG_SZ
Data: "C:\Program Files (x86)\Weather Watcher Live\ww.exe"