I've been having similar problems with a dated R4, and it doesn't seem to matter whether or not I'm using Ysmenu.
However, in my case, the game will load the first two or three times just fine, and then when I come back later to load it, it will hang on the very first white screen, and load no further.
For the sake of curiosity, I checked the md5 dealie for both the rom on my card, and the one I originally loaded, and they were NOT the same.
If this were a simple case of needing to be defragged, I'd think it would have affected my other roms on the card, but this has yet to be the case. Maybe I'm just unlucky.