$ uname -r
2.6.28-13-generic

First of all, I replicated your experiment with floppy.ko (although using 
kernel 2.6.28-13-generic) and got the same results --- everything *seems* to be 
working as it should.

However, I just used module-assistant to rebuild/install the modules
mentioned in my original bug (which had been obliterated on last kernel
update): these modules are tp_smapi and the custom hdaps that goes with
it. I verify that the new one is there (and so is the old one)

$ find /lib/modules -name hdaps.ko -ls
4786795   32 -rw-r--r--   1 root     root        29100 Jun 30 17:57 
/lib/modules/2.6.28-13-generic/kernel/drivers/hwmon/hdaps.ko
5668879   32 -rw-r--r--   1 root     root        31528 Jul 16 15:57 
/lib/modules/2.6.28-13-generic/kernel/updates/hdaps.ko

But even after manually running depmod -ae (and making sure that the file was 
actually touched after I did it), this is what I get:
$ grep hdaps /lib/modules/2.6.28-13-generic/modules.dep
kernel/drivers/hwmon/hdaps.ko: kernel/drivers/input/input-polldev.ko

Obviously I can't modprobe the new module (it tries to load the old one,
which doesn't work); but if I manually insmod it by pathname, it does
work.

So this is strange -- for some reason depmod (or one of its
"precursors") seems to be treating this particular module differently.
Unfortunately I don't know anything about how this stuff works and so
can't hypothesize about the causes!


** Attachment added: "incorrectly-generated modules.dep"
   http://launchpadlibrarian.net/29158298/modules.dep

-- 
/etc/depmod.d/ubuntu.conf ignored (updates directory not searched)
https://bugs.launchpad.net/bugs/389782
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