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Magnetic variation weirdness in the flight plan box
Is there something wrong with the flight plan box? It's disregarding magnetic variation for plan legs that start on GPS fixes. Example: http://skyvector.com/?ll=37.66236745592615,-121.62803122023934&chart=16&zoom=2&plan=A.K2.KPAO:G.37.477432099129075,-122.14122415511353:G.37.524253455722686,-122.0553653158545:F.K2.VPSUN:G.37.712581029756656,-121.52469148702943:A.K2.KTCY Shows, for example both true and magnetic course 056 where variation is around -14.
Thanks for spotting that. It's working now.
The problem seems to be back
The problem seems to be back now. The route below seems to show that the variation enroute from SFO to SAU is 17E. (355 true, and 338 magnetic?) Looking at the current SFO TAC it should be between -14 30' and -14 15'. http://skyvector.com/?ll=37.7277606740471,-122.16863294445855&chart=16&zoom=3&plan=A.K2.KPAO:A.K2.15CA:G.37.598797034023534,-122.4072686804235:V.K2.SAU:A.K2.KDVO:A.K2.KAPC
Not sure I understand you

From the link in your post, I do not find SFO to SAU.

I do see SAU to KDVO that matches 355T, 338M.

If this is what you were writing about, there is a good explanation.

First of all, let me be clear about what sources of data SkyVector uses. For all US flight planning, the current CIFP (Coded Instrument Flight Procedures) database is used. It is published by the FAA every 28 days in ARINC 424 format. The CIFP, formerly known as the NFD (National Flight Database), contains magnetic variation for all airports, fixes, and navaids. If you flight plan using an airport, fix, or navaid, SkyVector will use the CIFP value for variation. If you create a GPS or "user" waypoint, SkyVector will calculate the variation using the IGRF11 model for 0 MSL on the present day.

There is something important to know about VORs. In the CIFP, the magnetic variation value is actually not called variation, but installed declination. When they installed the VOR, they bolted it to the ground with a certain declination from true north. This probably matched the local area's variation at the time, but the local variation may have wandered since then. Changing a VOR's declination is a big deal. All of the airways using it and any fix defined by a radial from it will have to be re-defined. In some cases, Class Charlie and Bravo airspaces are defined by radials, so those will have to be redefined as well. Then there are all the approaches, departures, and arrivals that may have to be updated. Some may argue that is easier and safer to just build a new VOR nearby, give it a new freq and identifier, and change all the airways to use it. (see the ANC to TED conversion)

In the case of SAU, the Sausalito VOR, it was installed in 1965 with a declination of 17 degrees East. It has not been re-aligned since then. Notice in KHAF SAU SAC KSAC the heading from SAU to SAC matches the airway definition of 35 degrees.

So if you remember back to what I said earlier, that SkyVector will always use the value from the CIFP, it explains why you are seeing what appears to be a 3 degree error. If you don't like this behavior, don't select the VOR in your flight plan. You can create a GPS waypoint anywhere you like and you'll get a fresh variation calculation. But if you are outbound from a VOR, you will always be given its radial as your heading.

Thanks for the explanation.
Thanks for the explanation. I do understand the complexities of VOR placement. But they are not at issue here. Now that I understand what is going on, it seems confusing to have the numbers in the flight plan mean different things depending on what type the fix is. To wit, even the standard VFR nav logs have separate columns for the course to fly, versus true course, versus magnetic heading. Please consider explaining them better, or laying them out in a way that makes their meaning unambiguous. OTOH, maybe it's not such a big problem in general, as I don't see much clamor about this discrepancy on the forums. However, it will affect the way I use skyvector, but, of course, that is not of wider concern. Thanks, f