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I went to see Bendis' Avengers and found the entire thing marked as skipped. I changed the check all box to check them all an select "wanted". Only a few changed statuses. The rest remained skipped and I had to click them all manually.
I tried to take another comic, Avengers Vs X-Men, and mark them all downloaded, because they all said skipped, even a new one that wasn't downloaded yet, and get the error message "you didn't select any issues", wether i mark all or manually mark some. When the page was refreshed, some changed status, others remained "skipped".
I thought this was working at one point, but maybe one of the commit's broke something with the way it processes. I'll check it out...
Should be working now in latest commit 964338f