REGARDLESS of the code uploaded on the device (yes, even BLINK). I have had the same exact issue on 2 separate PCs, and 2 separate SparkFun Leonardo's. I too am having a problem with this device disappearing from the list of COM ports (Win7 64bit) in the device manager and in the Arduino IDE itself (v1.3). It is a bit unfortunate that they didn't add separate SPI lines to the shield headers the way they did with I2C, but they're starting to run out of space for adding more shield pins for the current Arduino form factor. Particularly with SPI, in which there's no flow control (unlike I2C with its clock stretching) Implementing PWM via software would have a greater impact both on the performance of the PWM feature and on the timing behavior of the user's code.
They went with the latter, of course, and I think it was probably the better option: Mostly when you use SPI on Arduino, the Arduino is the bus master - and bit-banging is usually good enough for the bus master of a synchronous serial port. So the choices were, either put the SPI port where it was before (losing the PWM feature on those pins), or put PWM pins there and lose access to the hardware SPI port on the shield header. On the ATMega32U4, none of the SPI pins have PWM functions. On older Arduino boards, two of the SPI pins (10 and 11) were also PWM outputs. Not sure which Arduino or Arduino-compatible board is right for you? Check out our Arduino Buying Guide! It contains everything needed to support the microcontroller simply connect it to a computer with a USB cable or power it with a AC-to-DC adapter or battery to get started. It has 20 digital input/output pins (of which 7 can be used as PWM outputs and 12 as analog inputs), a 16 MHz crystal oscillator, a micro USB connection, a power jack, an ICSP header, and a reset button. Also, because the 32U4 is handling the USB directly, code libraries are available which allow the board to emulate a computer keyboard, mouse, and more using the USB-HID protocol! Using the ATmega32U4 as its sole microcontroller allows it to be cheaper and simpler. The Leonardo is Arduino's first development board to use one microcontroller with built-in USB. Never fear for accidental electrical discharge, either since since the Leonardo also includes a plastic base plate to protect it!
The open-source IDE can be downloaded for free (currently for Mac OS X, Windows, and Linux). Arduino can be used to develop stand-alone interactive objects or can be connected to software on your computer (e.g. Arduino is an open-source physical computing platform based on a simple i/o board and a development environment that implements the Processing/ Wiring language.