Infield Fly redux

[Tru_in_Blu]

I searched some old posts and got some opinions on the following IF situation. I serve as the UIC for the particular league helping with their bylaws and rule interpretations. It is a company intramural modified league that does not allow bunting or stealing and otherwise utilizes the ASA rule set. Regular season games are 1 umpire games. Playoff games utilize 2 umpires. This happened in the first week of playoffs.

Visitors at bat in top of 7th trailing 8-5. They have runners on first and second with no outs. Batter hits a popup toward F3 who needs to backpedal a couple of steps. BU (who was in "B" because we utilize SP mechanics for these games) points toward the ball. PU did not call IF at the ball's apex, but did make the IF call in a low voice a few feet before the ball hit the fielder's glove.

F3 had the ball bounce off his glove while in fair territory. R2, not having heard an IF call then took off for 2B. When he was almost there, he saw R1 had not left the base. The throw to someone covering 2B motivated R1 to break for 3B. R2 was then tagged out and a subsequent play on R1 retired him off the base. This was ruled a triple play by the PU and ended the game.

Some background:
This field is very close to a major highway with maybe a couple hundred yards of light forest as a buffer. There is a lot of road noise.
The PU has had previous issues/complaints regarding IF such as not calling it at all, or calling it very late.
First base coach and on deck batter said they both heard the IF call, but that it was very late and not very loud.
BU confirmed the call was very late and that he did hear it primarily because he was waiting for it after signaling to the PU.
Umpires got together, but the play stood.
The losing team considered protesting the game, but apparently decided not to.

Had there been a protest I would rule that the umpire(s) placed the base runners in jeopardy. I'd rule the batter out on the IF and return the runners to first and second base.

Comments?