Kernel headers installed but not found

[Mark81]

Hello,
I was running Debian Jessie as Linux Guest, when I upgraded to Debian Stretch. I reinstalled the VBox Additions in this way:

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login as root
m-a prepare
sh VBoxLinuxAdditions.run

It fails because it doesn't find the kernel headers:

The headers for the current running kernel were not found. If the following module compilation fails then this could be the reason.
Building the main Guest Additions module ...fail!

But:

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uname -r
4.6.0-1-amd64

and:

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ls /lib/modules/
4.6.0-1-amd64

So the correct headers are available.
Inspecting var/log/vboxadd-install.log I found:

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grep: /lib/modules/4.6.0-1-amd64/build/include/linux/version.h: No such file or directory

Well, the path is actually wrong. linux/version.h is available under /usr/include/linux/ or /usr/src/linux-headers-4.6.0-1-amd64/include/generated/uapi/linux/.
It's a common behavior? How to tell VBox installer where to find that file?