System Information
Operating system: MacOS Catalina / Windows 7, Windows 10
Graphics card: RadeonPro 460 (Mac)

Blender Version
Broken: 2.80 OSX / 2.80 Windows

Saved Cycles render-enabled Blend file in OSX disables Transparent option when loaded into Windows.

Exact steps for others to reproduce the error
1 Open blender in OSX
2 Change Render Engine to Cycles & enable Transparent under Film section.
3 Set an output file with alpha (png, openexr) to save the sequence
4 Save the file
5 Re-open Blender in OSX & load the saved file
6 Render the sequence & check the output frame(s).

Result: Frame has included Alpha channel as expected with clear background.

7 Open the saved Blend file in Windows
8 Render the sequence

Result: Frame has solid alpha background, with colour set to whatever the world bg colour is set to.

9 Navigate to the Film section of the Render tab

Result: Note that Transparent is un-checked.

Workaround:
Check the Transparent box and re-save. Scene now has Transparent re-enabled.

NOTE 1 - I have not checked if this disables or re-enables is you re-load the scene file back into OSX Blender and re-save. It may break. Lost half a day on this when the render farm was outputting flat images!!

NOTE 2 - This occurs only in Cycles. Enabling Transparent in Eevee works as expected across platforms.

Thanks,

Pete