sometimes when you transfer the new files from the new firmware you accidentally do something wrong( this happened to me)
here is how i fixed it.
First you need to back up all your files but not the system folder and the other system files( ds_menu.dat etc.) if you want to keep your themes, cheat.dat and usrcheat.dat you can but do not save the whole system folder
then format your micro SD card
put all your files back on it then download the new firmware from the r4 site and put back your themes folder and cheat.dat and usrcheat.dat in system( if you chose to keep it) and it should work
note that this will only work if you don't include your system files and folder when you backup your files because other wise you will have 2 of every system file.
sometimes this may take many tries.
if this doesn't work this could helphttp://www.r4ds-forums.com/viewtopic.php?f=12&t=1354
i suggest my r4 gets stuck on loading screen(2nd from top), and the ds doesnt recognize r4( last one)
it may seem extreme but it worked
if anything you try here doesnt work then you probably have a FAKE r4. and you should third party firmware or YS menu.