headers in /usr/include are 9.1 but /usr/src/sys are 9.0

[Gary Aitken]

Using the generic kernel.
Some time ago I upgraded from 9.0 to 9.1 using freebsd-update.

originally, under 9.0, I had lsof installed (from ports).

Some time after all that I tried to reinstall sysutils/lsof and couldn't.
I wasn't desperate and ignored it...

Looking into it further, the problem appears to be the result of /usr/src/sys/sys/ containing 9.0.0 versions, and /usr/include/sys/ containing 9.1.0 versions.

I didn't think I had system source installed, but apparently I did.
I have vague recollections of telling the upgrade process not to upgrade
the source because I didn't think I had it installed; but maybe it doesn't
even ask.  I'm not really familiar with the process and it was a while back.

Anyhow...

1. Is /usr/src/sys/sys always present?

2. Do ports normally use headers from /usr/src/sys/sys instead of 
/usr/include/sys if /usr/src/sys/sys is present?

3. What's the best way to fix this?  
    freebsd-update fetch?

Gary