Hmm - works for me, have tested it on 5800 with Qt 4.6.3 and now also with 4.7.1.
Check that AutoStartApp_template.pkg has following lines in it:
Also check that c:\system\data\AutoStartApp.ini exists before rebooting the device.
; Manual PKG post-rules from PRO files
"C:/S60/devices/S60_5th_Edition_SDK_v1.0/epoc32/release/$(PLATFORM)/$(TARGET)/as_s60launcher.exe" - "c:\sys\bin\as_AutoStartApp.exe"
"C:/S60/devices/S60_5th_Edition_SDK_v1.0/epoc32/data/z/private/101f875a/startuplist.rsc" - "c:\private\101f875a\import\[e0123abc].rsc"
"" - "c:\system\data\AutoStartApp.ini", FN
Possibly you could add some debug logging code to s60launcher.cpp to determine if the StartL() function is called or not.
But if building & creating the sis package are both successful, then this has to be a certificate problem - although I don't know how to solve it. Maybe someone else with a developer certificate has tested the app?