thats weird as i have mine setup the same way with zombie gametype and ctf gametype running after one another on the same server but no problem arise and i dont have to use balance_teams command for none of the gametype as the way i have my events.txt setup it works perfect for me you can choose how many players join the red team b4 they start switching to zombies team just read up more on the zombie test server @ http://sapp.xgclan.com
by the way why do you even have to use balance_teams command? that would more than likely be used when you have team switching enabled in your gametype and ppl are switching to another team that already have more players than the team their switching from. if so be the case you can just add "block_tc true" to sapp's init file to block players from changing teams.
if not the case just put this in your events.txt:
event_start 'w8 5;balance_teams' and this should balance both teams 5seconds after each game. the 5 represents how much seconds after the game start, it would execute the 'balance_team' command, you can change it to the amount you prefer. hope this helps.
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