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.