Generally when I join a stackExchange site in beta it gives me a bonus 100 reputation to get started. Right now I am starting at 1 reputation. Is there a reason for this? Is this intended behavior?
It's not intended behavior, you should be getting +100. I tried reassociating your accounts and recalculating your rep, but it's not working; your log doesn't even show the account association happening. I tried creating a new account on an SE I haven't been on and got the same problem, so I filed a bug about it. Unfortunately there's nothing I can do in the meantime (I can't give you +100 rep); hopefully it doesn't affect you too much and it'll be fixed soon
Edit: One of the SO devs posted this on the bug report:
There's a bug in some new associations code (that went out last night) that prevents the current account from gaining the association bonus. This has been fixed on dev, and should go out tonight.
The work around for now is to establish the association from one of your other accounts (may require clearing before hand).
If you want the bonus now you can do the workaround (clear your associations here, go to another site, and associate with Unix that way), or just wait until the fix goes out and you can reassociate from here