If FMLA begins after one year employment, does the 6 weeks taken count in the first year or can only be taken after the first full year?

In other words...if FMLA kicks in after week 52 and I have to begin my maternity leave at week 46 of my employment does the 6 weeks I want to take for maternity count toward my first year or not.

I am afraid I will not have my job when I return unless FMLA kicks in.

Based on your post, you would not qualify for leave under FMLA. One of the conditions is that you be employed at minimum 12 months with the covered employer. You must meet all criteria not just some of them to qualify. Your employer may permit leave but they are not required to do so under FMLA. Since you do not qualify, it's *possible* that you could be let go as a result. You cannot be fired for being pregnant; but you can be fired in spite of it.

http://www.dol.gov/dol/topic/benefits-leave/fmla.htm

You will become eligible once you meet the 12-months employment. Then you will have 12 weeks at that time for pre-natal appointments, birth, recovery.