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@Gordon
That's odd - GC is actually extremely quick (just a few milliseconds) so I doubt that's the issue. Since Serial and USB share the same input buffer, could it be that there's just a big flood of data, and the serial buffer gets so full it can't even accept characters from USB?
Glad it's working with pipe anyway - since effectively 512 bytes get buffered, you've got ~44ms at 115200 baud in which to write the data out (in practice it's less though). How are you connecting the SD card? Is it possible that you could get a bit more out of it using hardware SPI with a higher baud rate.
Having said that, hardware SPI uses interrupts to handle the received characters, and it's possible that those interrupts end up blocking the serial interrupts and you lose data. You could try with software SPI, which might be a tad slower but wouldn't use interrupts so might mean you don't end up losing data?