When you update the R4 firmware files, make sure to delete the "_DS_MENU.SYS" file that the old firmware created on your flashcard when loading a new firmware for the first time. The file is 4MB. 1.08 will create a new one automatically the first time it loads the flashcart. Put all your goodies in place (games, apps, etc), but make sure you leave at least 4MB for the first boot for the "_DS_MENU.SYS" file to be created.
Maybe, if you didn't delete that "_DS_MENU.SYS" file, or didn't have enough free space for the "_DS_MENU.SYS" file to be re-created, the firmware wouldn't initiate properly and resulted in the issues you described.
Don't know if that will help you or not, but it's something to remember when updating the firmware files.