If your high limit screw is improperly set, the intermediate shifting will be erratic if you set the cable tension based on the high to second shift. I'd go back to square one with the derailleur set up.
Disconnect the cable, set both limit screws correctly, shift the brifter's up shift lever (inner lever in the case of Shimano STI shifters) multiple times to be certain it's in the smallest cog position, reconnect the cable and adjust the tension to get clean shifts in both directions.