A lot of people signed up for Nectar because it is 'better than nothing' unfortunately the way that it is implemented at Virgin is crazy.
Book on virgintrains.co.uk and receive Nectar points on Virgin Trains (West Coast) services only.
Book on virgintrainseastcoast.com and receive Nectar points on Virgin Trains East Coast services only.
That means if you want points on a Virgin Trains service you need to book on the correct site. If you don't you get nothing.
But there's an easier way. FirstGroup offer Nectar points on all rail travel, it doesn't matter whether you're travelling First, Virgin, ScotRail, indeed any operator you will still receive the same Nectar points.
Therefore the safe option if you really want points is to book through a FirstGroup site. Your points will build up faster as all rail travel will be included.
The FirstGroup sites are
Which site you pick doesn't matter, if you're already signed up with one use that. Normally I recommend Great Western as it has a memorable address: gwr.com
All you need to do is enter your Nectar card number in your profile like you did with Virgin Trains East Coast and off you go, safe in the knowledge you'll get points on everything.
NOTE: we don't think Nectar is worthwhile at all, but if you do want the points it makes sense to go somewhere that gives you points on all purchases.