As far as I know the adverb comes before the main verb in a positive sentence:
It will probably rain today.
You are probably working too hard.
I’ll almost certanly see you next week.
But when to be is a main verb (not an auxiliary) the adverb comes after it:
There were probably about 150 people at the wedding.
You are probably right.
I was defenitely at home at 10.30
The adverb comes before the auxiliary verb in a negative sentence.
I definitely didn’t tell her.
She probably isn’t working hard enough.
I’m not a native speaker, but according to the rules the sentence You are probably right is probably correct and the second probably isn’t correct.
Agreeing all above, I would point out that ‘You probably are right’ (putting the adverb first) indicates a certain hesitation in expressing the probability.