Also observed that the flex based html application when preloaded is taking the flashinjector.swf file from the mm.cfg file using the statement "PreloadSWF=path of the flashinjector.swf file" and this is conflicting the AIR object identification by the TestComplete tool.
The following two statement just before the application invoke(since in my project i have to work on two application instances ,one is in Adobe AIR (desktop based) and the other is web based flex application,and it worked wonders!!
'Uninstall the Flashinjector settings
Call Options.FlashSettings.UnInstallInjector
'Install the Flashinjector settings
Call Options.FlashSettings.InstallInjector
This two statements is simple removing/inserting the preloadSWF statement from the mm.cfg file at runtime.