I see your problem.
5668879 32 -rw-r--r-- 1 root root 31528 Jul 16 15:57
/lib/modules/2.6.28-13-generic/kernel/updates/hdaps.ko
You meant to install that in /lib/modules/2.6.28-13-generic/updates
didn't you? :-)
kernel/updates is not recognised specially
** Changed in: module-init-tools (Ubuntu)
Status: Confirmed => Invalid
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/etc/depmod.d/ubuntu.conf ignored (updates directory not searched)
https://bugs.launchpad.net/bugs/389782
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