Sounds like there's either something wrong with the icons themselves (could be the exact size) or theres something wrong with your Mods folder. What's the filepath for the Mods Folder that you have? And also, whatever folder Mods is inside, do you have that correctly linked in the ModInfo.xml file?
Also on the custom icons, did you make sure either A. the items/Blocks are the same name? or B. the items/blocks are referencing the customicons property to display them?
First time I did and made some didn't show because of either one of the above. I had to do this because a lot of the custom stuff I added had no icons with it and had to create my own like vehicles for example most didn't have any type of icons to show was just empty or blank icons. For me, it was easier to just name the icon or pics as the same as the item/block.
Now if its custom icons for UIs or stuff like that you have to config those in the UIs and Styles or reference them.