That happened to me before too, but I can't remember if/how I resolved it. Do you think that CPU stuff you were working on before will have an effect now feos?
I looked a little deeper into why the previous game end glitch run wasn't working on BizHawk. The final dominoe to falll to get the game end call is a check of $0078. Things seem to match up before this point. I looked at what set this address and found this:
c109127360 i35451970 $E07A:C0 FF CPY #$FF A:03 X:00 Y:FF S:F5 P:nvUbdIzC
c109127362 i35451971 $E07C:D0 0F BNE $E08D A:03 X:00 Y:FF S:F5 P:nvUbdIZC
c109127364 i35451972 $E07E:A4 15 LDY $0015 = #$03 A:03 X:00 Y:FF S:F5 P:nvUbdIZC
c109127367 i35451973 $E080:B9 9E E0 LDA $E09E,Y @ $E0A1 = #$E1 A:03 X:00 Y:03 S:F5 P:nvUbdIzC
c109127371 i35451974 $E083:85 19 STA $0019 = #$D8 A:E1 X:00 Y:03 S:F5 P:NvUbdIzC
c109127374 i35451975 $E085:B9 9F E0 LDA $E09F,Y @ $E0A2 = #$3F A:E1 X:00 Y:03 S:F5 P:NvUbdIzC
c109127378 i35451976 $E088:85 1A STA $001A = #$9F A:3F X:00 Y:03 S:F5 P:nvUbdIzC
c109127381 i35451977 $E08A:BC 0B 05 LDY $050B,X @ $050B = #$0E A:3F X:00 Y:03 S:F5 P:nvUbdIzC
c109127385 i35451978 $E08D:B1 19 LDA ($19),Y @ $3FEF = #$FE A:3F X:00 Y:0E S:F5 P:nvUbdIzC
c109127390 i35451979 $E08F:85 78 STA $0078 = #$90 A:FE X:00 Y:0E S:F5 P:NvUbdIzC
c109127393 i35451980 $E091:C8 INY A:FE X:00 Y:0E S:F5 P:NvUbdIzC
$3FEF is palette data. It is different at this point between FCEUX and BizHawk but I'm not sure why at this point.
But since the current run syncs, I might not look too deeply into it.