the desktop.ini issue can't be solved by samba. That's because the contents of the "Start Menu" are located in different places, like within your Windows profile (roaming) and the "All Users" profile (local). Because the latter is located on your PC, there's no way for samba to interfere.
If they are located on your PC you can hide them using Windows Explorer. Check "Hide protected operating system files" under "Tools/Folder Options".
I am using Samba and I don't see any Desktop.ini, neither local nor on the Samba server.
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