Hi Idan, do you have any triggers in SFDC that change the owner? Just like Cathal, I've never seen owner changes because of running "sync Lead to SFDC" on Leads that are already synced with SFDC.
Also, there is often no need to call "sync Lead to SFDC" for existing Leads because changes will automatically be synced as part of the periodic sync. Often I put a "choice" in the "Sync Lead to SFDC" flow step that says "only if SFDC Type is empty", meaning that it will only run for Leads that are not yet synced to SFDC.
If you still see issues, file a support ticket and provide the list of 40 leads that changed owner. If it's something specific to your SFDC, we may not be able to help, but if it's something that comes from Marketo, we can do more detailed troubleshooting.