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Ugh, I wish people would stop using the FTDI chips for USB. They are unsuitable for multi-channel, high bandwidth, low latency data acquisition.

Back a few years ago when your choices were: Cypress, SiLabs, I forget who else; FTDI was the first one that could be made to work relatively trouble-free on all three major OS platforms.

What would you suggest as a replacement?

Built in USB (i.e. use something like the ATmega32U4) or a custom USB chip like they started doing with the Arduino.

I agree with you here, but it is easy to screw it up. Early Arduino UNO models had to have the USB bridge's firmware updated because someone forgot a compiler flag, which resulted in a difficult to troubleshoot bug that would effectively 'brick'[1] some boards. http://arduino.cc/en/Hacking/DFUProgramming8U2

[1] Not really bricked, but bricked to someone who is expecting an Arduino, and new to microcontrollers.

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