I hate to get mired in any of these discussions, but anyone who says that different FLAC encoders produce different sounding files is selling you audiophile snake oil. It's a lossless 1:1 codec, so what you put in is exactly what you get out, bit for bit. It's like suggesting if you compressed and uncompressed some pictures with WinRAR that the people in them would be better looking than if you did the same thing with WinZIP or something.
This is true. The one thing to look out for is that some of the unofficial encoders produce files that sometimes don't work everywhere. I've personally been bit by that a time or two.