First off, you did the right thing by switching to SMF. Personally, it's my favorite forum software.
Regarding your permissions issue:
Go to: Admin > Go to the "Members" block on the left hand side > Membergroups > Under "Regular Groups" select "Modify" next to Global Moderators > Visible Boards: Click on [ Show boards ]
Check to see if ALL the available boards are check-marked.
On another note, your "Staff" board is visible to guests. Did you intend that?
Also, get rid of the SMF logo next to your forum logo.
Open index.template.php of your theme: SMF11 > Themes > Your theme > index.template.php and find:
<img src="', $settings['images_url'], '/smflogo.gif" style="margin: 2px;" alt="" />
And remove that entire line.