Also having this problem...
I'm also experiencing this issue.
I need my client to be able to upload .gif, .jpg, or .png (with transparent backgrounds) images that are resized to 125px widths to fit the output table.
If I check "Web Images Only" on the first step, I am able to activate the resize image option. This is when I get the black backgrounds on .png files.
If I clear the checkbox on "Web Images Only" I get the proper transparent backgrounds but the resize image options are not available to me.
I'd appreciate any help with this as well, please...