Do you have QT Pro ? I suggested using Toast to go 48k FLAC->44.1 AIFF because I thought it was independent of whether you had QT Pro but if the options are greyed out I suppose it must not be. The quickest method would have been 48k FLAC->join with xACT and output 1 big 48k AIFF->downsample with QT but I was sure that would require QT Pro.
Unless you want to spring for QT Pro (comes in pretty useful but not as nice as free) I suppose Audacity will be your best option and I'd change the workflow to:
1) Make a cue file of the original 48kHz FLAC's with xACT.
2) Join them all up with xACT but output to one big WAV (Audacity seems to be quicker with them).
3) Downsample to 44.1 with Audacity.
4) Split the downsampled biggie according to your cue from 1).
The QT FLAC plugins only worked with QT 6 and the current ones only work with Ogg FLAC but if you can wait that long, QT in Leopard is FLAC compatible
Sorry to send you up a blind alley first time around but this will definitely work.
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