First off, adding a new directory for icons and splashscreens without warning is kindof... well... not nice.
Secondly, adding this directory and not allowing custom sound files and other things is kindof... well... short sighted.
Thirdly, you created a bug... it's a stupid bug... it's a bad programming bug... it comes from someone young writing code and an experienced developer not paying attention... it comes from really bad test suites.
How to Duplicate:
I've moved all of my icons and splash screens to the new directory. I have to modify the icons and remove the transparent background for the iOS platform... no biggie. On the 29x29 icon I saved it as a 50x50 and then tried to reset it in XDK. After getting the constantly annoying reminder that you have a new directory, I pointed to the 50x50 icon and XDK correctly told me that it was a 50x50. No problem. I reduced the icon to the correct size, saved it again, was prompted to overwrite, did so. Back to XDK, click on the 29x29 folder, select the new file and it refused to import it saying that it was a 50x50 file. I verified that it was a 29x29. Tried again to reset the image, hovered over it and windows shows it as a 29x29 as is illustrated here.
And XDK reports the image as this:
Importing images of other sizes and then returning to the 29x29 doesn't change this error. BUT if you exit XDK, restart it and reimport that very same image you get...
So, this tells me that someone is saving some file info and not examining each file based on that files merits... #rookie mistake.