Audio IN and OUT messed up - how to diagnose??

I've got a weird issue and wondering if anyone can help. I have a Mac Pro and yesterday got a good mic and a pre-amp for my son to do some recording on GarageBand. I also installed the CuBase software that came with the pre-amp. The audio in and out is very erratic. Sometimes it will record, and sometimes not. And it will not playback properly (yes, I double-checked my Output/Input settings in System Preferences).
The same problem is happening on the CuBase software (which is GarageBand on steroids).
HOWEVER, when I fire up iTunes, all my existing MP3s come out of the speakers (line out) and headphone jack just fine.
Anyone know if there are potential conflicts between the system and audio editing software? Or perhaps it's the sound chip on the motherboard?
Related question: Can you add a sound card to a Mac Pro? I know the chip is soldered to the motherboard, but wondering if I can bypass that by adding a sound card?
Thanks for any help.

I haven't spent much time with Garage Band and I haven't used Cubase since OS9..
But there may be settings right in the DAW software that sets the default ins/outs as opposed to having your system settings control where the audio goes..
Another thing to take a look at is Audio MIDI Setup in the Utilities folder. It displays the system sound settings in a bit more detail...
Currently, there might be 1 or 2 PCI-express "sound cards" out there, but your best bet would be to look for a USB or, preferably, a Firewire audio interface. There are many of these out there with a large range in pricing..
If you are getting serious about recording, you may want to look at some of the small format mixers which include a USB or FW output. The advantage of these small mixers is that they are like swiss army knives for audio.. they allow you to route and mix audio in all kinds of ways that you would never imagine until you actually need it.. Some include digital effects, usually some EQ on every channel, from 2-16 mic pres, etc
Another route, again if you are getting more serious, is to get a ProTools LE or M-Powered setup. This way you are getting "Industry Standard" recording software along with a selection of different audio interfaces to choose from depending on your needs..
Apple Logic is also Pro-Level Software for a great price, especially at the current pricing.. You still need an interface, though, to get the most out of it.
Browse around the computer recording section at www.sweetwater.com to get a good idea of what's involved..

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