Whenever I make it into the first generator puzzle room Clank seems to never have the thing that allows him to switch through the gadgebots. The only way for me to get it then is to close out of the game and reopen it. Is there some sort of reason why it happens?

Yes, it's been a while, but, afaik it happens when you've played as Clank in that playthrough already. Before Veldin day-to-night skip was found, we restarted the game in Phoenix, due to having to play Quartu as Clank in the beginning.

ahhhhhh, that makes sense. i completely forgot about that clank section. thanks!

When I was planning on running this category way back, I didn't initially get the one skip and that happened to me too. I thought I'd wrecked the save file at first.