What is the version of Laz and fpc you are using?
as an example, I'm using:
Lazarus version 0.9.31, SVN revision: 34510, with fpc 2.5.1, on a win32 -vista system.
As to the differences you found using cmp, I refer you to ludob's comment.
Might you have hand edited your windows unit1.lfm file, by any chance?