Is it possible that you never set the default boot time sound values in alsamixer as root after you ran alsaconfig when you loaded your pc up?
I'm thinking that maybe you didn't or it got wiped out somehow, when you get into X it restores your values from kmix, gamix or the like? I have a few audigy 2's and never had this.
I'd say put the pc into run level three (/etc/inittab) the default slack boot run level as your default, then power off.
Now we need to verify the sound levels from your power off state, so power on, then log into console as root, type alsamixer and see what the defaults are on cold boot. use arrow keys to adjust them and move between different types, use tab key to jump over and check/repair your capture settings to while your there, and space toggles things on/off. then hit escape key when done. then to store the settings, 'alsactl store' at command line.
the power off give the pc sometime to spin down your hard drives then boot up and see if that makes any difference.
other than that, maybe trying a different slot can help. creative cards really like to get IRQ # 5 and they prefer to be (well in my experience) 1 to 2 slots away from video card, no more. They definitely do not like to share,they are IRQ greedy
Check your mobo manual to see what's shared and stuck as shared by default for your pci slots. Sometimes disabling stuff you never need like a COM port can help. Be sure you have grounding strap on and unplug wires from box before pulling card. No cigar ashes either
GL