Why are some (all?) files bigger on Mac OS X?

A few years ago, Mac OS X Snow Leopard changed the size of a MB to the standard that mega is 1000000 and not the historical 1048576 [1].

So if you compare the actual number of bytes used by the files, it should be the same.

[1] http://reviews.cnet.com/8301-13727_7-10330509-263.html

Are you sure that you are always using the same unit ?

Some programs count bytes by multiples of 1000, others by multiples of 1024. This way, a file of one billion bytes will be 1000 000 000 bytes, or 1000 MB (megabyte), but only 954 MiB (mebibyte).

See http://en.wikipedia.org/wiki/Mebibyte