Humm. Weird. I'm confused too.
The rule you're probably referring to is 8.3.E, but it specifically does NOT apply in this situation (R1 was forced). I can't find anything in the ASA rule book or the case book that would support that call.
Maybe your ump was just having a bad night (it happens), failing to see a 3-4-3 double play s/he might have expected in his head. Brain farts happen, I know.
Or maybe there's another hole in the rule book. I'll let somebody else with more experience chime in here; but this one just doesn't register with me.
I woulda called both runners out based on what F3 (the 1st baseman) did, though, if that's any comfort to you (probably not).
Glad you won your game