The post of head of the collective presidency was never Abdic's to start with - Bosnian voters elected 7 members to the collective presidency, 2 Muslims, 2 Croats, 2 Serbs, and one "other". The members of the collective presidency then caucused and chose their head amongst themselves.
You will perhaps recall a similar discrepancy between popular votes and final result which occurred here in America back in 2000.
This is what the Sobaka site I posted earlier said:
In Bosnia's federated system, the republic was ruled by a rotating presidency of five members, and the one who received the largest overall number of votes would become its chair. Abdic outscored Izetbegovic rather handily (Abdic received 1,010,618, with a good share of support among Serbs and Croats, to Izetbegovic's 847,386, mostly among Muslims). For reasons which have never been adequately explained, Abdic abstained from taking the head of the presidency, granting it by default to Izetbegovic.