I use unison with the option '-fastcheck true' to synchronize two local
vfat partitions, each filled with about 60GB of data. Comparison takes
around 3:30 hours while the actual copy/delete is done within a few minutes.
It seems that unison still reads every byte of every file to determine
changes, or how else could it take so long?

I've done some tests in squeeze:

When the options

fastcheck=true
pretendwin=true

are present from the very beginning (before cache files have been
created in ~/.unison), fastcheck works as expected for vfat mounts.

If these two options are not present during the initial run, and only
added later, fastcheck becomes effective only after something was
changed and the change propagated by unison.  (This propagation somehow
seems to "convert" the format of the cache files.)  See also:
http://www.mail-archive.com/linux-users@it.canterbury.ac.nz/msg53365.html

I think, this could be considered either a "bug" or an "undocumented
feature".

Cheers!

Thiemo Nagel