Hi William! What user owns the /etc/smartermail and /opt/smartermail folders in your installation? Is it a specific user or are they defaulted to root? I suspect one of your JSON configuration files may not actually be getting updated.
I am having our QC team do a couple of test migrations from Windows-->Linux and vice versa to look for anything that we may be able to correct in that process, but I recommend submitting a ticket on this in the meantime so our support team can check things out with you and provide guidance.
There are a lot of areas you might run into trouble from permissions in Linux, to missing files or different pathing, so getting eyes on the environment might be our best bet.
Kyle Kerst
Acting IT Manager
SmarterTools Inc.
www.smartertools.com