Freqout resets port pins?

Im new to Pic Basic Pro so if this sounds stupid, sorry.

I'm using a pic 12f629 to sequence some leds on porta.0-2 and make sound on a speaker on porta.4. The sound changes as the leds sequence. I set the leds and then issue a freqout command. It appears that when I use the freqout command, port pins 0-2 are being reset too. This means that the leds aren't on long enough to see. I can do either the sound or leds separately but not together. Does anyone know anything about this or a workaround?