Starting a app as the last one doesn't mean the SDCard is mounted at 
this time.
However: Your Dependency problem is solvable using a additional 
SystemPath entry.
Read carefully:
http://msdn.microsoft.com/en-us/library/aa909187.aspx

Andreas Unger wrote:
> I tried to enter it into init as the last process to be started after 
> everything else. However, assuming that the OS does try to launch the 
> app at start up, it still wouldn't launch though because of the 
> dependency on msvcr90.dll. What I'm stuck on is how to add an 
> additional search path for shared libraries in the registry (sort of 
> like LD_LIBRARY_PATH in Linux).
>
> --Andreas
>
> On Mon, Mar 29, 2010 at 7:02 PM, Marco Borm 
> <[email protected] 
> <mailto:[email protected]>> wrote:
>
>     Typically the Startup and HKLM\Init is done before the mount of
>     external
>     drives is completed. So your starter has to wait until the relevant
>     drive is mounted.
>
>     Andreas Unger wrote:
>     > I did try putting in the absolute path of the application in the
>     > memory card (\Storage...) but that didn't work which is probably
>     > because the launcher application depends on msvcr90.dll. How can I
>     > edit the library load path in registry so that msvcr90.dll is found?
>     >
>     > --Andreas
>     >
>     > On Mon, Mar 29, 2010 at 7:23 AM, Oleg V <[email protected]
>     <mailto:[email protected]>
>     > <mailto:[email protected] <mailto:[email protected]>>> wrote:
>     >
>     >     Can't you just leave it in some other folder and use an absolute
>     >     path in the registry? Just try doing that first. Also, you
>     may be
>     >     able to use the QtConfig tool somewhere in tools to remove
>     >     unnecessary classes from your definitions and hence save space.
>     >
>     >     On Mon, Mar 29, 2010 at 6:00 AM,
>     >     <[email protected]
>     <mailto:[email protected]>
>     >     <mailto:[email protected]
>     <mailto:[email protected]>>> wrote:
>     >
>     >         Send Qt-wince-interest mailing list submissions to
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>     >           1. Auto-starting a wince application (Andreas Unger)
>     >
>     >
>     >        
>     ----------------------------------------------------------------------
>     >
>     >         Message: 1
>     >         Date: Mon, 29 Mar 2010 00:14:21 -0400
>     >         From: Andreas Unger <[email protected]
>     <mailto:[email protected]>
>     >         <mailto:[email protected]
>     <mailto:[email protected]>>>
>     >         Subject: [Qt-wince-interest] Auto-starting a wince
>     application
>     >         To: [email protected]
>     <mailto:[email protected]>
>     >         <mailto:[email protected]
>     <mailto:[email protected]>>
>     >         Message-ID:
>     >
>     >        
>      <[email protected]
>     <mailto:[email protected]>
>     >        
>     <mailto:[email protected]
>     <mailto:[email protected]>>>
>     >         Content-Type: text/plain; charset="iso-8859-1"
>     >
>     >         Hello,
>     >
>     >         I have a Qt application in a memory card on a Windows CE 5.0
>     >         device. How can
>     >         I get it to run automatically when the device boots up? I
>     >         intended to create
>     >         a launcher application that starts the main application in a
>     >         QProcess and
>     >         place the launcher application in the \Windows folder, then
>     >         edit the
>     >         registry but I don't have enough space in the \Windows
>     folder. My
>     >         application has a size of 992 KB while the space
>     remaining in
>     >         \Windows is
>     >         only about 800 KB.
>     >
>     >         I suspect that a Win32 application would be much smaller but
>     >         I'm not
>     >         proficient enough in the Win32 API to get the launcher
>     to work.
>     >
>     >         Any ideas on how I can get this to work?
>     >
>     >         Thanks,
>     >         Andreas
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