Great news! Ans's method Nes/Emulation Speed/Set Frameadvance Delay-9999 worked :)
I managed to tas and
sync the beginning of my new files. I verified by chosing one file for all 9 runs and it picked correctly all 9 bosses. Though curiously, even though my batch file works perfectly fine does not seem to load the save state. I get the error message: "State 1 load error". Can anyone determine what the problem might be? This only happens when I do this procedure via the batch file. If I manually open 9 fceuxs, I get no error call and it loads the save state just fine. Here is yet again how my batch looks like:
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Mega Man (U)-0.fm2" "Rom/Mega Man (U).nes".
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Mega Man 2 (U)-0.fm2" "Rom/Mega Man 2 (U).nes".
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Mega Man 3 (U) [!]-0.fm2" "Rom/Mega Man 3 (U) [!].nes".
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Mega Man 4 (U)-0.fm2" "Rom/Mega Man 4 (U).nes".
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Mega Man 5 (U)-0.fm2" "Rom/Mega Man 5 (U).nes".
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Mega Man 6 (U)-0.fm2" "Rom/Mega Man 6 (U).nes".
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Mega Man in the Mushroom Kingdom-0.fm2" "Rom/Mega Man in the Mushroom Kingdom.nes".
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Rockman 2 Gray Zone-0.fm2" "Rom/Rockman 2 Gray Zone.nes".
start fceux.exe -readonly 1 -pause 1 -playmovie "Movies/Rockman 5 - Wily's Dream Space (J)-0.fm2" "Rom/Rockman 5 - Wily's Dream Space (J).nes".