Yes, the LED's are correctly oriented. I have desoldered and resoldered some of them to no effect. The interesting thing to me is that in all the rows that are effected the leds stop working at a point and continue down the row. If it was due to the soldering I would think that it would be more random.
I work with some electrical engineers and they said that I might have damaged "the common." I am going to bring the board into work for them to take a look.
Any other ideas?