I just solved my problem - it turns out r4i-gold.com does not have the right firmware updater file, which should be up3dsv42.zip. Some google searching led me to find that file on r4i-gold.eu, and I used that to update on a ds lite (keeping the original kernel files from r4i-gold.com). This time I didnt receive a msg telling me it was already updated, and it went on to update successfully and now works in my 3DS
In other words, if you want to update your R4i Gold 3D from r4i-gold.com, you need to use the kernel from http://www.r4i-gold.com/en/download/skin/2012/0115/282.html and the updater from http://r4i-gold.eu/downloade.asp named up3dsv42.nds. Hope this helps anyone with similar problems as me.
In other words, if you want to update your R4i Gold 3D from r4i-gold.com, you need to use the kernel from http://www.r4i-gold.com/en/download/skin/2012/0115/282.html and the updater from http://r4i-gold.eu/downloade.asp named up3dsv42.nds. Hope this helps anyone with similar problems as me.