See MWE below. The symbol ! in the \index causes an error. This is only the case in align environments (not in equation). So it seems to have to do something with amsmath. If ! is put in an \mbox ...
The .ilg file is fulll of errors, and no \index command is accepted. This is makeindex, version 2.15 [TeX Live 2011] (kpathsea + Thai support). Scanning input file thesis.idx... !! Input index error ...