I have two songs that mp3gain (1.4.6 - used with track gain and clipping allowed) fails to adjust correctly:

1. PJ Harvey - Rid of me
2. Jefferson Airplan - White rabbit

Both songs begin quietly and reach a crescendo at the end. When you listen to them on CD the beginning is very silent, barely hearable, and the end is a bit louder than the general sound level on the album. However, when listening to them on my iPod the beginning of the tracks are at a (perceived) level equal to the average and the end unbearably loud.

The songs gain adjustment are quite different, Rid of me's gain is increased with 3.1dB while White rabbit's gain is decreased with 4.7 dB.

I understand what track gain means. In those two cases mp3gain should try change the gain so that the volume in the middle of the songs match rather than matching the most silent part.

Any ideas on how to work around these issues?

I'm not sure about that version of MP3Gain but you could always choose a different target db level for the gain. In your case try removing any MP3Gain/Replaygain and use Track Gain on just that track alone to see if you can reach something that fits with the rest of the album, yet is pleasing by itself as well. I have an album where two of the tracks are so quiet in respect to the rest that after album gain is applied they are reduced even further and might as well be silent with the default MP3Gain/ReplayGain settings.

Sorry but that doesn't make sense. If "White Rabbit's" gain was decreased by 4.7dB then it will be 4.7dB quieter at the begining, 4.7dB quieter in the middle and (surprise surprise) 4.7dB quieter at the end.

What doesn't make sense?

You said the beginning of the song was louder after a decrease of 4.7 dB.