Okay, so, there's actually a few things that happen with this game's score that are quite wonky for a puzzle game.

First of all, the in-game score counter only shows five digits. (And thus, it caps to 99,999)
However,  the score count itself does not cap at 99,999. It counts up to a six-digit number, because at the end of each round, it will show your current accumulated score in six digits, along with the tally of how much of each combination of block pieces you included.
So, the last point of which you can capture your score is at the end of round 8. I think it'll show you results at the end of round 9 as well, I'm not sure, please correct me if I'm wrong with this ^^'
And if you happen to lose in the game, it will show only five digits of your score, yet again. So, if you're going to get past 99,999, but NOT make it to the end of the stage, you should screen shot in-game for your 99,999. Then the quickest 99,999 will count for you.

I know this is a little complex to abide by, but the score display system is a little finicky, and there's not much we can really do about that.

Now, good luck out there and have fun with Quarth, just like I did!