Hi Lyndon,
Nobody has reported a problem to us regarding this setting not being saved correctly, and I cannot duplicate this in sample data and Ledger 9.2B (2017.03.20). Being able to set this is not particular to a security setting, as if the user is allowed to edit accounts, then that user will be able to edit the Restrict to Subledgers option and select the various subledgers on the special tab.
On the account master record, there is a field labeled 'Restrict to source codes' that you can add to the account grid with the column editor. If you edit an account and enable 'Restrict to subledger' and one or more programs, when you save the change, is the value of this field Yes or No on the grid? If Yes, then the value is being set correctly - and if editing the account again shows the checkbox off, then that value is being reset for some reason. If No, then the account is not being updated with the change. Remember that I cannot duplicate either or these in sample data.
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Regards,
Softrak Tech Support