To clear things up, the part of the scoring algorithm that is important here is what they refer to as BonusScore.
Essentially the first half of the score for a note is calculated by dividing the maximum score (1 million) by the number of notes in a song, and then scaling the score based on what judgement you got.
The second half starts by doing the same thing, but it also multiplies it by a special "bonus" number. The bonus number is a bit confusing to explain, but basically if you hit anything less than a 300, it will go down, and a miss will make it 0. It goes up slowly for every 300 or max you hit.
When you miss, and the bonus drops to 0, you actually get almost half as much score on your next hit. It takes 50 max's (or 100 300's) in a row without any lower judgments to raise the bonus back to maximum. This has a VERY big impact on your score.
Also, don't worry so much about score. Since the score calculation is.... not ideal... you'll encounter cases like this pretty often. As long as you keep getting better, you'll still be able to improve you scores on songs over time. Plus, improving a score on a ranked map doesn't give you a lot more PP once you've reached something like 800k score on that song.