BSc vs MSc

I'm a graduate, currently working as research assistant. I have
completed my BSc Agriculture special Degree (GPA 2.72/4.00) and MSc.
in Molecular and Applied Microbiology (GPA 3.95/4.00). My MSc. degree
duration is one and half years and don't contain research component.
However, I have two years research experience (as a research
assistant) and I have two local research publications.

I have several problems.

1) I did my MSc degree to compensate negative effects of low BSc GPA,
but now I have a doubt about validity of my MSc. (Because 1.5 years
and 31 credits)
2) What should I do to reduce the negative effects of low GPA?
3) In order to get scholarship in molecular biology /biotechnology (or
research assistantship) what should I do?