Would it be possible to use the latest edition when pricing out cards in decks? It throws off the value a lot for cards like rolling earthquake, or anything recently reprinted when it uses the first printing.

Yep, mostly we use the latest printing. We don't though for some special sets like from the vault.

Which cards did you see this happen for? (high discrepancies between original & new printing in a special set - not in a core set or expansion)

FTV and Commander.

For FTV it makes sense to use older printings (although pk3 reprints create some weird pricing issues, like rolling earthquake).

For commander releases, the new prices are much lower. For example, sapphire medallion.

For example, the commander precons come out about $30 higher on here than they really cost.

On a related note, would it be possible to automatically price all basic lands at zero?