Whenever Minecraft is restarted or a new Resource Pack is selected, volume settings are reset. The sliders appear to be set at previous level, but sound is much louder. As soon as the main volume is adjusted, it corrects the problems.
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Cannot confirm on 13w42b.

Check again because I can confirm this is still a bug in 13w42b. Just tried. Set your sound to 15%. Close Minecraft. Load Minecraft again and select 16%, you'll notice the clicking sound is much lower when you refresh the sound slider.

Ok, can confirm with master sound level, but not with the individual levels.

Oh right. I only had the issue with the Master.
I can confirm this as well.
Confirmed for 13w42a. Although I'm the issue without loading resource packs. When I set the sound level to "15%", close Minecraft, then reopen MInecraft, the sound level shows "15%" but the game is obviously louder until I move the slider.