I have tried creating a new giveaway using one of the keys that had no entry winner (I have another spare key for that game anyway, so if there was an issue where a winner needed a key, but it had already been used by someone else, I could let them have the unused one. However, the website won't let me create a giveaway for using that key. This suggest the website may have a system in place where it checks if a Steam key has been used in a giveaway before and prevents it being used multiple times.
This could mean that the keys we put into giveaways are lost, at least for the purposes of Indiegala giveaways, as they cannot be reentered again. This is a bit of a shame as I was pushing on to my next Indiegala level and lost quite a few XP points.