Hi. I have a simple configuration here, so this should be easy to reproduce.
I have the hoe (golden hoe) mapped to instant action Y.
If I hold Y, it takes noticeably longer for the tool to charge from one square, to three, then to five, then to nine squares.
After I have hit Y (and the hoe is selected), when I hold X, the tool charges through those levels much faster.
I hope I'm being clear. Holding Y works, it just works more slowly. Holding X, the interval between each charge-up is far shorter (quicker).
This is not a high priority issue.
Thanks again for this fantastic mod!