Ugh.looking at your spritesheet the icons clearly don't line up on the spritesheet therefore they won't on the style since the original icons line up on the spritesheet and on the xf default style.
Ensure you've placed them exactly where the original icons were and you will have the icons aligned correctly. What I do is add the custom icons on the sheet, make sure they are lined up and in the correct place and then i delete/erase the icons (xf) on the sheet keeping your custom one on there. This will serve as a guide so you know they'll line up.
Clearly I am doing something wrong. My icon doesn't look like the same shape as the icon on the right. I made the image 10px x 10px and the cicrle inside 8px cuz 9px or 10px was too large.
Here is an enlarged image of the sprite spreadsheet. There is no way to get them lined up since they are different shapes. I wish XF would provided the PSD files of every image...but they don't.
Here is the image of thee actual size after placing the new icon in the spreadsheet...