Changed unattended install to use "setup.exe". Same issue, software installs without shortcuts or group. However if we manually run setup.exe the program group and desktop shortcut install. I've pasted the contents of setup.ini for reference.
******************************
Application=PL/SQL Developer
AppSuffix=
AppClass=TPLSQLDevForm
ExeName=PLSQLDev.exe
ExeDir=PLSQL Developer
ExeArguments=
WorkingDirectory=
SetupDescription=
ReqMB=30
Version=100
ReleaseDate=01122012
;registration details for aapf library
[aapf.dll]
AppID={0D8AFBD1-C447-4C1E-8D2C-25699076ED3E}
TypeLib={DD5BCA8D-5511-47CF-9B96-8EBBC5482AA9}
LocalizedString=-101
ProgID=aapf.PrivilegedObject
Version=1.0
[register]
Name=PL/SQL Developer
Description=PL/SQL Developer file
Command=
Icon=1
;Files from previous versions
[delete]
PLSQLDEV.HLP
PLSQLDEV.CNT
PLSQLDEV.GID
PLSQLDEV.LOG
command.kwf
html.kwf
java.kwf
plsql.kwf
sql.kwf
xml.kwf
debug.txt
plsqldev.elf
plsqldev.log
;The section below allows you to control the installation procedure.
;Read the included install.txt file for detailed information.
[AutoSetup]
Silent=true
LicenseAgreement=false
Language=
Path=
CreateGroup=true
CreateGroupIn=
CreateShortcut=true
TemplateFiles=true
KeywordFiles=true
ExternalExecute=
AutoStart=false