Yes. There are three minor things to keep in mind:
A) It is best to have the .mbl, .xmbl, or .cmbl extension on all files, so they are recognized by Windows as Logger Pro files.
B) If you move Mac files to Windows, they will work perfectly as long as they have the extension.
C) If you move Windows files to Mac they will work fine, but their icons will not appear correctly. You can fix the icon problem by using an application like File Typer, or you can open the file in Logger Pro on the Mac and then resave it.