yes, drain it ,
take that nut off, hoping that some simple reason explains why it's leaking
there...
like insufficient goop, or not tightened well enough....
 though seems unlikely that you'd miss torqueing  one nut while torqueing
down that head.

I have never had the need, or even heard of, sanding the bottom of the nuts
flat. I've installed hundreds of those nuts that didn't leak.
I put a pretty generous amount of goop on them , including inside the nut
where the threads are.
I assume you cleaned the threads of the studs and nuts fairly well.......and
very lightly oil the stud threads ...right ?
 since goop goes on those threads I try not to make them real oily ...but
not bone dry .. the nuts need to turn nicely during tightening.

I can't say I've ever had one leak ...
so here's hoping it's a simple workmanship thing, and not a crack in the
head there or something thing like that.
If ever there was a cylinder head system that requires pretty meticulous
workmanship ...it's waterboxers..
but the nuts and goop are not the tricky part...so you really shouldn't have
a problem there.
let us know what you find.

Scott
www.turbovans.com

----- Original Message -----
From: "Roger VanTill" <motelvw@GMAIL.COM>
To: <vanagon@GERRY.VANAGON.COM>
Sent: Wednesday, April 28, 2010 3:54 PM
Subject: Leaking head nut

>I rebuilt my 2.1 this spring. Was very careful, read everything I could,
> watched Ben's videos, etc. Got the motor and new tranny installed. Filled
> the system with coolant this afternoon. It's sitting there, not started
> yet,
> unpressurized. I've got a coolant leak coming from one of the upper center
> head bolts on the driver side. Tears are still falling as I write this.
>
> Yes I sanded the bolts flat and cleaned up the mating surface on the head.
> I
> used the yellow goop that came with the gasket set.
>
> Should I just drain it, remove the leaking cap nut and reseal it? Do I
> trust
> the other 15?
>
> Looking for advice and a pat on the back to tell me it'll be alright.