According to neuron2 one of the programmers for DGIndex, the D2V format has changed. GordianKnot is not able to parse these D2V files and subsequently won't use any media scanned with the 1.4.9 versions of DGIndex from here on out.
Sample from a newer .d2v file:
E:\Voyager\Season 1\Star Trek Voyager - A1995.01.30 E104 - Time and Again (DivX v22.214.171.124 AC3 SUB HD1200)_1.vob
E:\Voyager\Season 1\Star Trek Voyager - A1995.01.30 E104 - Time and Again (DivX v126.96.36.199 AC3 SUB HD1200)_2.vob
I have tried editing the "DGIndexProjectFilexx" to 13 and it will result in GK opening the file, however I don't yet know the effect it will have on the rest of the encoding process.