What size of upgrade are you putting in? Putting in an upgrade doesn't make it run faster, just cover a larger area - so a standard 3x3 will complete its pass after only checking 9 squares, a 10x10 will have to check 100 squares (the unmodified version will have checked its 3x3 area over 11 times in the same amount of time). You may just have to wait long enough for it to reach the appropriate area.
If in doubt, plant a straight line of oak trees from one side to another leading from the harvester straight out - bonemeal the oak trees until you have a solid wall. You'll be able to see its progress every time it crosses this line so you can see it work. Check the planter itself to make sure it's actually running down its idle timer - if it's getting a redstone signal it'll stop and hold until the signal disappears.
