I used the embedded index feature in Acrobat Professional 8 to add an index to several large (up to ~200 MB) PDF files; the output files created were up to 600 MB. All looked good until I started trying to search for text near the end of the files. That's when I discovered that the indexing was not complete on some files. For example, on one of the files of 164,502 pages the indexing stopped at page 163,397. It seems to be related to the size of the files or index because none of the smaller files had this problem. Any ideas?
Apparently the problem was not with the index being incomplete but with the reader. I downloaded Adobe Reader 9 and it finds the text near the end of the file.