When the phantom power is on, some channels decide to come and to. Particularly with the SM57 mic

Did you turn on the phantom power? Condenser mics need phantom power(unless the have their own battery.)

There is really no way for a condenser mic to damage the board UNLESS you break the ground and get a static discharge into the input. That can happen with any microphone and has NOTHING to do with the phantom being on or off. As phantom power goes on and off slight bias at the input preamps can make amps non-linear causing the raspy sound you heard. The Phantom LED means NOTHING as it shows the state of the phantom switch by connecting a 12 volt source through a resistor to the LED... It shows NOTHING regarding the state of the 48 volt supply. Each input circuit has two 6.8Kohm resistors to the swinger of the phantom switch 2nd pole that either grounds those or connects them to a filtered 48 volt source. As long as you don't have a static buildup there is NO need to turn phantom power on or off while connecting a condenser microphone. At each input when using the XLR jacks are two per side 470pf capacitors for RF bypass. For the XLR's there is a 10Kohm between the signal lines and two series 10mfd/50 volt caps in series of each input to block the DC, when using phantom power, from reaching the preamp stage. These caps have to charge and discharge when changing the state of phantom power so you should AVOID having the main amps being driven while changing the state of any phantom power. Always have the fader(s) down and any monitors down to avoid a thump and also the non-linear raspy transition as the input caps charge/discharge. So fix the microphone... don't know what type you have, but DO check the cable (first) as ALL three conductors MUST be good for a condenser mic to work on phantom power. A ground leakage or noisy connection will cause your symptoms. Use a SHORT known good cable right at the board to test the mic. The 48 volts is applied through the two 6.8K resistors between both the signal lines to the shield of your XLR cable. The microphone picks off the 48 volts with a similar circuit.
Now let's cover a very important thing regarding system safety: ALL, and I do mean ALL interconnected equipment MUST be powered from the same source. Professionals run a power cord back to their mixer right alongside the snake. This is to avoid ground bounce damage due to bad building grounds or ground faults.

Sorry, but the Lexicon Alpha does NOT have Phantom power and you can't use a condenser mic with it without a Phantom power injector or preamp.
If you mean you have a Phantom power injector then it should be working. Do you have seperate mics for the two channels of the stereo? If you have only one mic, then only one side will record unless you set for mono recording and then dump the recording into stereo voa Cubase. I would recommend you get a small mixer... even a 4 channel one to use ahead of the Lexicon so you can mix and PAN your mics the way you want them. The recording and trying to control the panning in Cubase can be frustrating... The Lexicon really doesn't have anything built in to PAN the mic to the center when stereo recording. Small mixers are inexpensive and often you can find them used or in pawn shops for cheap.

Sorry, but the Alpha does NOT have Phantom power which IS required for a condenser mic.

You will either have to get a mic preamp that supplies phantom power or go to a dynamic type mic if you stay with the Lexicon Alppha.

Assuming you are connecting a microphone to this, if the mic is a condenser mic, make sure you have Phantom power on the PreSOnus turned on. You have given us almost no info of your configuration of mics and other devices connected to this unit.

Sorry, but the DI-100 can OPERATE on phantom power, not supply it. If you have a mixer that has phantom power then you have no need for the DI box. DI boxes are to convert unbalanced signals to balanced to send via XLR or TRS cables.

If you don't have a mixer that has built in Phantom power or a source of Phantom power, then you need a mic preamp that can supply the phantom power.

Here is an example device, but DO shop[ around as you should find some even less expensive. Make sure they have phantom power.

http://www.amazon.com/M-Audio-Audio-Budget-Microphone-Preamp/dp/B000CZ0RZG

This sounds bad... I suspect that a noise suppression cap on one side of the bad channel has shorted... possibly due to a static discharge.
Test for this doing this: Using a meter, with nothing plugged in and phantom on, check the voltage at both pins 2 and 3 to pin 1 of the XLR connectors. If you find either pin 2 or 3 is much lower than its mate (they both should be 15 volts to 48 volts positive), then one side noise filter cap probably has shorted. Unless you are electronically adept at repair, take it in for servicing.

I assume you are using CONDENSER microphones, as these are really the only ones that can use Phantom power. Also do NOT use any MONAURAL connections to MIC jacks while using Phantom power.

Make sure the mic/line button is selected when trying to input from teh external inputs.

If it is brand new, it is likely "pilot error" as setting these up if you are unfamiliar with mixers can be frustrating.

There are several things that must be done to have a working system. Correct speaker cables are one and the setting of all the knobs are important...

DO NOT REPLACE FUSE. If any LED's are on, fuse is OK. If fuse blows, service the unit before replacing fuse to avoid further internal damage.

Make sure speaker cables are good.

Set the level control for the channel you are testing up AND you may need to press the "PAD" button to change the input gain. Turn up the master gain.

Depending on the source you are using, line or mic you may need to change the PAD button.

NOTE: This mixer does NOT have Phantom power and cannot be used with CONDENSER microphones requiring phantom power. You will get no audio from a condenser mic without phantom power. You must use dynamic mics with this mixer.