When you're monitoring the audio of a Real Instrument track, the audio input monitoring may stop working after about 90 seconds into your recording session. You may hear clicks and pops in the monitored signal before it drops out.
This issue affects GarageBand versions earlier than 3.0 (which is a part of iLife '06) when using different audio interfaces for the input and the output. For example, if you use an external USB or FireWire audio interface for input and your computer's built-in audio for output, this can happen to you.
To avoid this issue, use the same audio device for both input and output when using an affected GarageBand version.