That's a myth. He actually had a supermajority for like a month.

Al Franken's seat was caught up in a lawsuit for a long time, and by the time he was able to take office Ted Kennedy got sick.

Instead of resigning he just stopped showing up for months, stalling everything until he died. His seat was filled temporarily by the governor in late 2009 and the Senate broke the Republican fillibuster and passed a shitty Healthcare bill right before the holiday recess that was supposed to be cleaned up in reconciliation with the House bill.

Then the Tea Party happened and took Kennedy's seat in the special election, so the Dems only had 59 seats and couldn't break another fillibuster. At that point the Dems could either give up or the House could pass a verbatim copy of the Senate bill so it wouldn't have to go back to the Senate after reconciliation with the House bill.

So the broken Senate bill had to be passed in the House, and that's what went to Obama's desk.