Important: During this upgrade you need to format N-Card/clone, please backup your games and saves first!
1.Insert the Writer into slot 2 and insert N-Card into slot 1.
2.Use USB cable connect to PC USB port directly. (Please do not use extension USB cable)
3.Hold "up+L+R+A+B" while starting your DS, now you should enter upgrade mode(a red colored text should appear).
(4. Extract the Firmware Archive.... It's more safe if you have it in a directory than trough a packer program)
5.Double click "NAND_ALL.bat" to run upgrade program. Please ignore if there some "found a badblock" appear when upgrade some 8G dslinker.
6.When it finished you will have to Quick Format your N-Card by holding DOWN+A+B+L+R when starting your DS.
7.After formating you have to copy "xmenu.dat" from here to the root (main directory, i.e. N:/ ) , If the xmenu.dat isn't on the card you won't be able to enter the Menu.
8.After the first time enter "GAME MODE", DSYSTEM folder will be set up. This folder you must not delete, or you will get an error when starting.
Now your N-Card/Clone should be updated ;D
I can't guarantee that this'll fix your problems, I really don't know what your problems are. And I'm quite intrigued as to why anyone would think an R4 update would work on a NAND-based card...