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Perhaps the problem lies in the fact that the battle is conducted differently during a siege and in an open field, even with the same army. Some extra weight or other action might change the turn order of the units. Take a closer look at your battles. I described the turn order in a post on this site, and it might also be detailed in the guide for Heroes of Might and Magic III in my signature.
Техника в руках индейца мертва.
Справочник по НоММ-4 http://handbookhmm.ru/pamyatka-dlya-heroes-iv.html
Памятка по НоММ-3 http://handbookhmm.ru/pamyatka-dlya-homm-iii.html
и HotA http://handbookhmm.ru/vyishla-obnovlennaya-pamyatka-dlya-homm-iii-hota.html
Справочник по НоММ-4 http://handbookhmm.ru/pamyatka-dlya-heroes-iv.html
Памятка по НоММ-3 http://handbookhmm.ru/pamyatka-dlya-homm-iii.html
и HotA http://handbookhmm.ru/vyishla-obnovlennaya-pamyatka-dlya-homm-iii-hota.html