1) Do you think the QA exp wont be counted?
Not much. It's a completely different activity done with a different mindset and different tools. I don't see how QA experience would help a developer,
2) Does switching from mnc to startup company for skills development will affect a resume?
I don't think it so, but I think it's easier to switch from QA to development within the same company than switching company and departments at the same time. If you stay at the same company, you already know the purpose of the code being developed/tested and you (hopefully) have some knowledge about the domain. So I'd either stay at your current company and switch departments, or apply for a new QA job and try to switch later. (That's why interviewers sometimes ask "where do you see yourself in 5 years?")
3) Does a small profile project looks bad on resume,after 2 years of experience.
I don't know how to answer that. Your projects be compared to the projects of other candidates.
4) What does a manager looks in a candidate's profile? previous Company? previous project? or skills he/she has developed?
Yes, yes and yes.
5) Does a software development in a non-it company counted?
Of course. Most software development is probably done at non-IT companies.