I have a condenser mic, and it needed phantom power to work, so I bought the Ultra Di-100, but I don't know how to make my mic work with it.

Phantom should ONLY be on if using CONDENSER mics or a DI box requiring phantom power... yours should be OFF. cables should be correct. The 2 Trk to mix button should be down.

Chances are there is nothing wrong with the mixer. IF you accidentally turned on Phantom power, that would cause the problem. Phantom is ONLY used with condenser mics and a few DI boxes. Turning it on can create noise unless balanced lines are used everywhere.

Don't know what you are saying. Phantom power is only used for Condenser mics and a few DI boxes. Make sure you ONLY use TRS or XLR cables into ANY/ALL inputs when using Phantom power. Please describe what you mean by :some channels decide to come". ONLY change Phantom power when system is off as you will get loud noise often by switching phantom while live.

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.

HAve you tried a different lead? Try a friends mic that you know works on your mixer. Its usually a process of elimination. You substitute a known working one and see what happens. Is the little LED lighting up when its turned on?

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.

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.

Sorry but... Very simply, you CANNOT use a condenser mic with the Alpha since it does not supply the required Phantom power for the mic. You must step up to another interface to use condenser mics. You can use dynamic mics with the Alpha or other audio sources. I use a Roland/Cakewalk UA25E interface with condenser mics and also the Lexicon Omega which does have Phantom power for the mics..

Make sure you have Phantom power turned on on the Lexicon... Oh,oh... it appears that the Alphs may NOT have phantom power which IS a REQUIREMENT for most condenser mics...

The Lexicon Omega does have this but apparently the Aplpha doesn't have it.

That leaves you with the choice of either getting a dynamic mic that doesn't need Phantom, or replacing the Alpha, OR using a preamp ahead of the mic before the Alpha...

Sorry, but those are the only solutions I see for you.

REMEMBER that condenser mics pick up everything and you cannot run them into a PA or they will feedback.