The Ubuntu packages are not just a drop-in. They hook into DKMS which the 
Nvidia drivers themselves do not do. There's also a lot of other Ubuntu 
specific things that the package does. Looking at all these bugs they all have 
to do with the module failing to build with the Ubuntu package. I don't see 
any reports of the issue with Nvidia .run installer.

On Thursday, January 15, 2015 08:29:12 PM Brian Norris wrote:
> The Ubuntu package is mostly just a drop-in of the official Nvidia
> packages for Linux:
> 
> http://www.nvidia.com/object/unix.html
> 
> So yes, this is actually an Nvidia upstream problem.
> 
> I suspect that there is some sort of race condition in the provided
> build scripts written by Nvidia, and they are only showing up
> intermittently or under particular system configurations/states, so
> package reinstallation tends to work fine the second time.
> 
> Related: I see this comment in Nvidia's Makefile regarding the "new"
> build system in Linux >= 2.6:
> 
> # The new approach currently has its own share of problems, some of which
> # are architectural difficulties with KBUILD, others minor annoyances. For
> # this reason, an improved version of the NVIDIA Makefile is available to
> # those experiencing difficulties.
> 
> So it sounds like they admit to having architectural difficulties here.
> I wonder where this "improved version" of the Makefile can be
> obtained...

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https://bugs.launchpad.net/bugs/1268257

Title:
  nvidia-331-updates 331.38-0ubuntu3: nvidia-331-updates kernel module
  failed to build, with only error: "objdump: '... .tmp_nv.o': No such
  file"

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