I've had this happen a couple times when I haven't gotten all the slack out of the cable. As a result what you think is the highest position on the shift lever is actually the second-highest. After doing this a couple times, I discovered this process:
My process for adjusting the derailleur and cable tension on indexed shifting systems:
Detach the cable.
Verify that moving the derailleur by hand moves the chain across all the cogs. Adjust the "L" and "H" screws so this is as far as the derailleur moves.
Shift the shift lever into the "highest" gear. Verify that the cable is fully seated in the shift lever and all of the cable housing is fully seated in their stops.
Manually shift the derailleur so the chain is on the second-smallest cog. Don't turn the cranks further- let the derailleur hang
Connect the cable to the derailleur, pulling out all the slack.
Verify that turning the cranks allows the chain to shift to the smallest cog. Fine-tune with the barrel adjuster so shifting between the smallest and second-smallest cog is consistent in both directions. Work your way up the cluster, shifting between adjacent cogs. Fine-tune as you go. If everything is in good working order you should be able to reach the largest cog when the shifter gets to it "lowest" position.
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Jeff Wills
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