I'm pretty sure... It worked one day and the next it didn't. Based on the message itself I thought it might be a problem with some sort of internal indexing, resulting in an attempt to load a lump which doesn't exist. i.e. load lump #x, which is > the total lumps therefore it doesn't exist.
Maybe I'll start transferring stuff one section at a time and see when it stops working.
Your WAD is referencing data that does not exist but the engine never does a proper check for that. Without the WAD creating the error it will not be easy to locate.
Do you have any backups of your wad handy? If you use XWE or Doom Builder at all to edit it, they regularly back up your data by default (though I believe the former only does it when you hit the "clean wad" command). Try using an older version and see if it works. I'd place my bets on wad corruption -- not a pretty sight in either case.