Could you provide the generated modules.dep file, along with an output
of "find /lib/modules/2.6.28-13-generic -ls" and "uname -r"

This works when I try it:

# grep floppy.ko /lib/modules/2.6.28-14-generic/modules.dep
kernel/drivers/block/floppy.ko:

# cp /lib/modules/2.6.28-14-generic/kernel/drivers/block/floppy.ko 
/lib/modules/2.6.28-14-generic/updates 
# depmod -ae

# grep floppy.ko /lib/modules/2.6.28-14-generic/modules.dep
updates/floppy.ko:


** Changed in: module-init-tools (Ubuntu)
   Importance: Undecided => Medium

** Changed in: module-init-tools (Ubuntu)
       Status: New => Incomplete

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