My Area51 account crossed 200 rep today, but still other accounts don't reflect the change in reputation. When will the changes be applied? or is there no association bonus for Area51 account?
Area 51 is different from the Q&A sites.
It is a completely different beast.
Reputation gained on Area 51 doesn't indicate that one has gained knowledge in how the Q&A sites work and operate, just in how Area 51 works... so it shouldn't give you a reputation bonus on the Q&A sites.