I can confirm this problem and that it is still present in Maverick.

I've attached my amixer output before and after switching inputs back
and forth - but they are identical.

It would seem there is something that is initialized correctly by
switching between inputs that is not initialized correctly on initial
startup. I would suspect this might be an issue either with the MCP55 HD
Audio driver, or the specific implementation of it on this motherboard
(I have the same motherboard "ASUS P5N32-E SLI PLUS ACPI BIOS Revision
1502").

Windows seems to do this correctly (so it's not just a hardware issue).

** Attachment added: "amixer settings before and after"
   
https://bugs.launchpad.net/ubuntu/+source/pulseaudio/+bug/577178/+attachment/1698138/+files/amixer.7z

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nvidia mcp55 p5n32e-plus soundmax microphone only works after switching to 
another input setting and back
https://bugs.launchpad.net/bugs/577178
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