About what did they charge you direct from Lexus, if you don't mind me asking?
I bought some of the same keys for my wife's GX. Had the same problem. Ended up buying keys from Lexus and didn't have a problem programming them.
I now have a tool to read the transponder in the keys. The keys from Amazon have a 4D68 tp30 tag which is for Toyota. They come up on the reader as a Toyota master key. What the Lexus uses is a 4D68 tp29 tag.