Preview mode (which it sounds like you are running in) is a single window containing three panes; the folder list on the left, the message list in the upper right, and the preview pane in the lower right.  List mode, or "Classic" mode as it is referred to in the manual, is a separate window for the folder list and for each open folder.  A message must be opened to be viewed (this mode works best for me). 

It wish I understood what else is at play that is causing the "Remember and apply each folder's sorting mode separately" option to affect the sort order of the New Mail folder. 

Thank you for your feedback.

A few years ago I posted something about this and got a reply that suggested I delete or modify a file.  It fixed the problem.  I searched for the messages but could not find them.

I'm running 4.7 now.  All messages in the New Mail folder sort on Open in alphabetical order in the From column (all other folders sort by Date/Time).  I want to sort the New Mail folder by Date/Time.  If I click on Date/Time it does sort but it does not stay there.  When I exit and reenter, it sorts again by From.

Is this option enabled?  Tools > Options > Incoming Mail > Preview mode settings > Remember and apply each folder's sorting mode separately

Also, if you allow read messages to stay in the new mail folder unread messages will be displayed at the top of the list whenever the new mail folder is first opened regardless of the sort order.

Yes, the option is enabled and yes I was aware of the unread messages appearing at the top.  The thing is I only resort my incoming mail every week or so and so it would be nice to have it automatically sort properly as I tend to remember the day a message was received more readily than the sender's ID.

As I said, someone did give me a fix which required doing something with a file.  That is what I am looking for.

The HIERARCH.PM file holds the folder info including the sort order but the new mail folder is different from any other folder so I am not sure whether its sort order is stored in HIERARCH.PM.  Keep in mind that a rebuild of this file will result in the loss of any tray structure.

From Hans' Guide to Pegasus Mail Filenames and File-Extensions:

HIERARCH.PM:  "This file contains the information about the individual settings and profile for each folder. The sort order, the unique folder id, not only for the actual mounted mailbox but for all mailboxes once mounted are stored in this ASCII databasese file."

[quote user="alsandor"]

A few years ago I posted something about this and got a reply that suggested I delete or modify a file.  It fixed the problem.  I searched for the messages but could not find them.

I'm running 4.7 now.  All messages in the New Mail folder sort on Open in alphabetical order in the From column (all other folders sort by Date/Time).  I want to sort the New Mail folder by Date/Time.  If I click on Date/Time it does sort but it does not stay there.  When I exit and reenter, it sorts again by From.

[/quote]

See if this helps:

http://community.pmail.com/forums/thread/42264.aspx

Thanks for the link.  It gave me an idea and I tried it.

I unchecked "Remember and apply each folder's sorting mode separately" in Tools | Options | Incoming Mail | Preview Mode Settings.

All folders now sort by Date/Time.   I exited a few times to make sure and it is "fixed".

I would be interested to know if the sort behavior reverts back if you re-enable the setting to remember each folder's sorting mode. 

Also, are you operating Pegasus Mail in Preview mode or List mode?

Revert back?  Yes it does.

> Preview mode or List mode

Not sure what you mean...I have both a list and a preview panel open.  It's what works best for me.