yes...only the 1st place person advances.
Understanding Tournament format

From the home page of the tournament. So tell me why with 3 players in 2 groups, only 1 from each group advanced. It clearly states that 2 players advance.
Players: | 100 | Time Control: | 24 hours/move | |
Max Group Size: | 4 | Rating Range: | <1500 | |
# Advance: | 2 | Tie Breaks: | Yes | |
Points Available: | 535 | Games Rated: | Yes |

I suspect this is the reason:
No more than 50% of each group can advance, unless there is a tie for the last advancing player, or there is a larger group within that round.
So, despite having a 4-player per group for the entire event, you were placed in round 6 in two 3-player groups. With no ties, only one player can advance, since 2 advancing players would be larger than 50% of each 3-player group.
Had there been a 4-player group alongside the 3-player group within the same round, then two players would be allowed to advance for each group since the placement of players in the 3 and 4-player groups is random, and players shouldn't be punished for being in the smaller group.

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But @alidad is correct, the maximum number that can move through is 50%, barring ties, and later rounds will not have more members per group than the largest of the previous round.
Was just in round 6 of a tournament noted 4(2)->2
Nearing the end of the tournament, with 3 players in my group, I thought coming in second would advance me to the final round, but no, 2nd and 3rd place were eliminated and only one player advanced. Can someone explain this to me?