Am in a process of automating custom add-in (built in C#) operations in MS Word 2007 using QTP9.5 with .Net add-ins.

Since QTP does not record accurately on Word, using VBScript I build few functions like Launch word, loading/creating documents, searching for commandbar buttons (custom addin buttons) and I could able to replay these functions against Word successfully.

Whenever my VBScript function does click custom add-in button in Word, Word launches a Window (settings for custom add-in). QTP does not identify this window in replay, If I stop the VBScript execution then QTP does identify the Window.
The window is like
Window("Microsoft Word").SwfWindow("Settings")
Whereas my requirement is to do some settings at replay and continue further.

Can somebody let me know why QTP does not identify the window in execution?