Probably it's just a glitch - I have checked and it seems that I can connect as Commander on HC server without any issues (via PC). Were you trying to get on Rush servers by any chance? These have Commander disabled by default now.
Then it probably is some sort of a new bug, as I can find these servers and join them properly via Battlelog on my laptop. Still, could you please post all the search settings that you chose (region, number of players etc.)? I honestly doubt that it's search-related, but it wouldn't hurt to try.
