A picture of the ballot for the 1999 East Timor vote on independence is available here:
Without delving into the question, it is a well designed ballot. It is in colour and has pictograms for illiterate people, it is written in four languages (English Portuguese, Tetun and Bahasa-Indonesian), and has arrows and coloured areas showing where to vote.
That having been said, the question is very confusing. The ACCEPT option is to remain part of Indonesia, while the REJECT option is for East Timorese independence. One would normally expect the "Reject" option to be for the maintenance of the status quo.
Second, the pictogram is confusing. The independence option shows East Timor connected to the rest of Indonesia, while the autonomy option shows the territory of East Timor on its own, quite the opposite of intuition.
Finally, I find the "Accept" option describes the legal arrangement incorrectly: "Do you ACCEPT the proposed special autonomy for East Timor within the Unitary State of the Republic of Indonesia?" My reading of the autonomy plan ( http://www.etan.org/etun/annex.htm ) have been for a special autonomous region with powers set out in "constitutional framework" annex of a treaty between Portugal and Indonesia, ie., having the force of internaitonal law. A unitary state is one where all power remains with the central government and any power that it does not exercise is merely delegated and can be revoked at any time. This could have led to misunderstandings had this option won the vote.