You should answer "Yes"

You should answer "Yes" since your employer has filed immigration petition on behalf you (or yourself if NIW). It does not affect H1B visa application.

I just came back from China. I am holding H1b. My I140 was approved on Feb, 2006(within a week after submission).

I got security background check in Shanghai Consulate. But this has nothing to do with I-140 petition. It was because of my teaching and research area which is sensitive and has military applications.

it took a month for the investigation to get cleared.Finally I got the visa stamp.

Hope I can file I-485 August. My priority date is July 8, 2005.