If he turns invincible that's because the time window after he hit the bomb has ran out and/or he hasn't hit the bomb correctly. As for the autosplitter everyone has trouble with it at first.

Superskip%. A super skip run uses the mr krabs e spamming glitch to start the "kill mr krabs in his final form" quest. Then by shooting Mr Krabs you're able to complete that quest without triggering the boss fight. Technically you never "lower his health bar to zero" so it doesn't fit in to any%.

Have you cleared your save data between runs?

There's also an alternative "Super skip" run that isn't yet recognized by speedrun.com. It allows you to complete the "kill mr krabs in his final form" quest without having to do the boss fight. Hopefully they add it as a category in the future.