I'm seeing similar weirdness. I'm running a Wondows domain with a domain controller which is also a WINS and DNS server so my situation is a little different, but here's what I'm seeing:
My media shares are all shared out with access to the user Xbox. In the network settings I've told Boxee to use my workgroup, username and password. It does connect to my media shares, but like you it doesn't seem to scan them automatically every hour like I've told it to. I have to hit the refresh source option, and then it adds the media to my library.
But another weird thing - With the last release, I was able to browse SMB shares that I didn't have "mounted" already. These shares did not allow access to the xbox user, so when I clicked on them I would enter a different username and password, and I could browse them with no problem. But with the latest release I'm seeing the same thing you are - I keep getting prompted for a username and password over and over. Not sure where the issue is, and I've been too lazy to check the security logs of my Windows servers to see what credentials Boxee is passing.
I have lots of computers.