Rear shifting woes - running out of options

My rear derailleur isn't shifting very consistently, particularly across the smaller 5 cogs on the 10 speed cassette. What I've tried so far

• checked rear hanger alignment with Park Tools alignment tool as well as removing it and checking it on a flat surface
  
• new inner cable and checked it was moving smoothly through all the housing
  
• cleaned rear derailleur and made sure it was moving smoothly
  
• checked wheel alignment and that the cassette was tight on the wheel
  
• adjusted cable tension but can only get either reliable shifting up or reliable shifting down but not both
  
  
  

I'm running out of ideas for what could be causing my shifting problems. I've managed to get it to the point where it shifts through most gears apart from a couple of the middle cogs where I need to move the shifter until it clicks and then give it a little extra nudge, before it gets to the second click, to encourage it to shift up.

By the process of elimination, assuming the cable and derailleur are fine then it must be the shifter, however it appears to click through all 10 positions fine both up and down. I've read about lots of cases of Shimano shifters jamming up and not clicking through at all but never of one having uneven cable pull between indexing positions?

Anyone have any other ideas as to what else it could be?