This may sound a bit extreme, but it would not be a bad idea to completely remove the cable and re-install.

If you do this, here's the drill:

1. Remove cable.
2. Up shift the shifter all the way (click with small lever until it stops clicking). The hole that goes through the brifter should now be lined up properly with the cable housing. This is VERY important.
3. Now, insert the cable by pulling on the brake and inserting the cable straight in from the side of the STI housing - just like you're trying to poke the cable into the housing, but the brifter is inbetween.
4. Push the cable through and route to derailleur. Make sure you get the cable anchor head seated completely before you do anything further.
5. Perform everything already discussed above.

EDit: If your cable is frayed, go to LBS and buy a new one for $2. That's a lot cheaper than replacing your brifter.