Many states start with your Federal AGI and subtract items that don't belong to that state from there, so since you hadn't yet entered all your Federal info, your West Virginia Non-Resident return was not yet accurate.
When you're done with Federal entries, go through the West Virginia interview again and pay close attention to questions asking about income that needs to be subtracted/adjusted. It sounds like this is what you were doing. The tax you paid to West Virginia at the time of the sale was only a % of the estimated Capital Gains at that time, so you could have additional tax due.
Here's more info on West Virginia Sales of Real Property by Non-Residents.
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