Thanks for your feedback! The placement of the custom blocking wizard is a feature, not a bug. :) The wizard used to be shown at the top of the page. Ads can appear anywhere on a page. If the ad was near the bottom of a very long page, the wizard would "disappear." By keeping the wizard at the top of the screen, however, it at least remains within view regardless of where the ad is placed.
It takes a tiny bit of time for the wizard to disappear while the new filter rule is being created.
You can selectively change a filter rule. In AdBlock's options, visit the CUSTOMIZE tab. The box under Manually edit your filters contains all the custom filter rules either you or the blocking wizard have created. Click Edit and then delete the rule that blocks the ad you want to unblock. Be sure to click Save afterward.