Jeff Wittrock (wittrock) reports that SetBaudRate is documented to have no effect with FT245 and other devices in FIFO mode, and specifying 48M as the baud rate actually yields an error.
I wonder why this hasn't been reported before. Actually, AFAIR, I had it running with the UsbBlaster driver before (but maybe that's just a wrong assumption and I only tried it with FT2232, never with FT245)
http://sourceforge.net/forum/forum.php?thread_id=1982021&forum_id=682993
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ftd2xx.c SetBaudrate to 3E6 instead of 48E6: Committed in rev. 1178.