Sometimes the PC or Mac drivers are not actually ready to begin receiving data immediately after they cause DTR or RTS to assert.  This delay allows the PC to become ready before we tell sketches the Serial device is true (ready).

This patch simply checks if NUM_ENDPOINTS is defined, and will bypass the
built-in USB descriptor, device and memory code, and allows a custom setting.
This bug does not affect the IDE unless someone adds the custom option to
the boards.txt file, and provides replacement code in a library or sketch.
It can also be used to turn off USB by providing no replacements, while
allowing speeds >= 20MHz.

http://forum.pjrc.com/threads/25350-Teensy-3-1-Serial-Break

http://forum.pjrc.com/threads/24726-Teensy-3-0-Serial-available%28%29-bug?p=42926&viewfull=1#post42926