Tile editor blanking over my edits

When editing tiles it keeps blanking over my edits. Ie, I color a quarter of the tile and it reverts to the default color.

Yeah there an issue with the auto-saving feature of the NESMaker tool... it looses/reverts some modifications :S
It will be deactivated in the next version to come (until they find why this is happening).

So, in the mean time, save often... and double-check all your modifications.

Interesting. That makes sense though. Look forward to the next release.