Virgin are devils for this.
It can often occur as a result of 'clustering', where the 1st class Advance fare from one station to several dozen other stations is priced the same for simplicity, but the walk-up price differs.
For example, Nuneaton to Stoke is £46.30 on the day, but the most expensive Virgin 1st class Advance is £41.00, the cheapest £13.50.
Birmingham to Stafford is £15.80 on the day, but the Virgin 1st class advance prices are the same, with the most expensive being £41.00, the cheapest £13.50.