It has to do with the Sandforce controller on the Toshiba Drive. It's really fast for compressible data (think text), but it slows down considerably when it has to deal with uncompressible or already compressed data (think mp3's, video files).
Filevault comes into play because the encrypted data can't be compressed, so it's treated like uncompressed data. Write speeds on the Toshiba drive will drop from around 350-400 MB/s to around 250 MB/s!
The Samsung SSD uses a different controller which doesn't have this issue.
However, as I said earlier, this only deals with write speeds. So both drives can read data at about the same rate. This is where the speed comes from when booting, opening apps and opening large files. And unless you are working with large files quite often, you are not likely to notice the speed difference.
The biggest problem is the perception of having "the best" machine. Especially on MR, people like to make a big deal out of every little thing. Some are big deals (such as random core shutdowns on the early Airs and image ghosting on the new Retina displays), but most are just making mountains out of molehills.
Hope this helps.