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I am guessing from your question the problem is that your local Windows machines have both a local profile and a profile on the Linux server, which
I also assume is running Samba. I assume that the problem is that you are finding yourself with both a local Windows profile and one on the server. I won't presume to be the expert in configuring this but my friend John Terpstra has written an excellent How-To on this subject. The detail is probably exactly what you need.
I think for your particular case you need to decide if you want support for
Roaming Profiles or Local Profiles. Roaming profiles will synch the local settings from the Samba server acting as a Primary Domain Controller. You can also disable Roaming Profile Support so that you only use the local settings on your PC. The Profile Management How-To at the link above should help you make these decisions.
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