Just a quick update on this issue--the problem was that the missing methods were "insignificant methods" (methods that contributes less than 1% of your application's total CPU time). Unfortunately, insignificant methods are not exported when you export the call tree though, I've created a feature request for this with reference PP-3343. Many thanks to Hien for the suggestion!
(Just a note: in version 8 of the profiler, you can actually export the methods grid to html *with* the insignificant methods included, so long as the "Hide insignificant methods" box is unchecked)
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