I have Unison 2.40.63 on both Windows and RHEL, all configs are working fine except when I try to run it first time it gives
Fatal error: Internal error: New archives are not identical.
Retaining original archives. Please run Unison again to bring them up to date.
First, just to cover our bases, I would check to make sure the same version of Unison is getting called on each machine. Unison 2.40.63 may be installed on both machines, but maybe there is a different version hiding in the PATH being called first. See unison -version.
That's probably not the issue though. This was a bug that cropped up before using older versions of Unison. See here and here. If I understand right it's because the versions of Unison were compiled with different versions of OCaml. Anyways:
There are much newer versions of Unison available. Unless you have a good reason to, I would upgrade. I'll bet this will solve your problem.
If you really really want version 2.40.63, then on each machine you'll have to first compile and install OCaml 3.12.1 from source, and then compile Unison 2.40.63 from source with OCaml and install it. This is what I had to do awhile ago to get things working with this version of Unison.