Solution: Buy a separate audio interface dedicated solely to monitoring.
I know this is an old thread, but I had the same problem, and was able to glean the solution by reading several similar threads. From what I could gather, it seems that if your audio interface is used for both your input (e.g., microphone, guitar, synthesizer, etc.), and your output; i.e., you're using the same audio interface to output sound for monitoring (e.g., through a pair of connected studio monitors), Logic produces a "loopback" effect, where all of your previously recorded audio tracks in Logic's timeline will also "print" (record) onto any newly recorded audio tracks.
Again, I had the same problem until I bought a separate audio interface, dedicated solely for monitoring, an M-Audio M-Track 2X2M class-compliant USB audio interface ($149). I chose this one because it looked cool, was inexpensive, and is a class-compliant USB device (so it doesn't need a driver to work). I assigned the M-Track 2X2M as my "output device" in Logic's preferences/audio menu. I only use the M-Track 2X2 interface to send audio to my Yamaha HS5 studio monitors from its two 1/4" phone jacks on the back. I don't use any of its analog inputs (or else I would produce the same loopback problem).
[Note that in my particular case, all of my input devices are hardware synthesizers (e.g., Korg Kronos) all of which support sending a digital audio stereo-pair + MIDI data over USB, so I don't need an audio interface for any of my inputs.]
http://studio460.com/images/mtrack-6.png
M-Audio M-Track 2X2M
http://studio460.com/images/lhelp2.png
http://studio460.com/images/lhelp1.png