Going from Madrid to San Sebestian in Jan and wondering if people could weigh in on this subject. What's best train or bus? Have taken train before, its longer I believe, but ok....get a little nervous putting luggage up from. Seems bus provides more security as they are stowed down below.

Try Iberia...may be you get the low cost. last time only <25 Euro for me and took only 1 hr.

The Bus ride Madrid to San Sebastian in January could be something you don't want to encounter: Mountain Passes closed because of snow. I made that drive (San Sebastian - Madrid) in January once in the middle of a snowstorm when all the northbound Buses were stopping in Burgos and the southbound buses were grounded in San Sebastian.

Even the Trains were stopped until the tracks in the high Passes could be cleared. I had to detour San Sebastian-Tolosa-Pamplona-Tudela-Soria and finally to Madrid.

Have you considered flying Madrid-Bilbao (usually cheaper fares) and busing to San Sebastian or just flying Madrid-San Sebastian??

mmmmm... I'd say bus, Continental-Auto from Avenida de America. I have done the trip often during winter, and the chances of a serious blizzard exist, but it's a matter of luck.
I've done the trip during jan-feb dozens of times and I only have had slight snow troubles a couple of times.
The rest of the time it has been riding trough the Madrid sierra under the sun and into the inmaculate white snow... a priceless experience. Imagine the Velazquez blue skies above and the snow white below... magnificent!
I mean, this is not Finland or Minnessota, it can snow heavily for some hours and then everything goes back to normal. This happens regularly every winter from northern Madrid to the northen Spain mountains, but road traffic is only slightly distorted.
And man, Continental Auto drivers are very efficient in winter driving!
A serious blizzard that traps you let's say for a couple of days or three is very uncommon, only once in a few years.
The worst thing that could happen normaly is a couple of hours delay.
For example: last March all the buses heading north from Madrid were trapped all night by a blizzard in the Burgos province. Sports pavilions were enabled for the troubled passengers to spend the night there.
This was the kind of heavy blizzard that you must be very unlucky to encounter.
Go for the bus!
No pasa nada!

Thanks for the suggestions. I guess I will play it by ear once I get there. I have taken the bus before, but its longer and more espensive. If there is snow (lots of it) then i'll ride the rails, if not take the bus.