I did not even know until recently that the 2 were even different.
@ZeNiX, I understand 
You and aaron are CN, right? I can help you, maybe another mod like mr.exodia will verify what I say...
We will use the two buttons as following soon.
[Add Reputation]
[Thanks]
Also, as I explained before, [Thanks] gave one reputation point in the past.
Newbie user can collect enough [Thanks] to be promoted to VIP by a
[Happy New Year] or
[Happy Birthday] post. I know this is a mistake of promotion rule. So, we tried to make changes to avoid such kind of mistake.
I did not know about these "New year" and "Happy Birthday" posts... where can I learn more?
I think the change to Add Reputation and Thanks is a good one but still needs further clarification for new members. As an english native speaker, it just doesn't make sense to have a seperate button for "Thanks" and "reputation" -- by your description, Thanks is more valuable than reputation, but it doesn't seem to be working like that..?
My suggestion is to keep "Add Reputation" -- remove "Thanks" - merge them. Reputation == thanks.