Why doesn't system see audio input (jackplug)

I have an acoustic guitar, attached to my Mac Mini (Lion 10.7.3) via a guitar pickup by a jack to audio input, with output to external speakers. System prefs are 'Audio line in port' and 'headphone port' - the only choices - but it doesn't even 'see' the input - there's no response from the input volume bit. I can play itunes, dvds, cds through the external speakers, but not hear anything attached via the audio input. I tried through garageband, and set the audio according to instructions, but even with 'hear playing while recording' set, I can't hear it.

I had been able to hear the guitar through the speakers before I (unfortunately!) had to reinstall Lion. This may be part of the problem: I forgot (yes, I know - daft!) to install Snow Leopard first. However, I do have it on another partition, which seems to be sufficient as in all other respects Lion so far is working fine.

Any help or suggestions would be greatly appreciated. I'm hoping I'm just simply missing something obvious.

Thanks.