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They will, as do most skimmers, need to work a little bit and re break-in so to speak. Whenever I do a complete clean with mine it takes a little time for it to adjust. Mine does pull out a good amount a dark brown sludge, but will still bubble through the top hole as you've described.
HTH :D...
Yes,
The bubbles you see are the last product of your denitrification process and are free nitrogen. They will rise through the water column and disperse. Part of the gas exchange going on in your tank.
:D :) 8) :lol: :o
HTH