Finally I have had access to a Samsung handset to check why PhoneMarks doesn't work!
Bad news, for the moment. The Samsung device uses a customised version of the stock browser (as I thought). This customised version allows creation of 'folders' within the bookmarking list. When PhoneMarks updates your bookmarks, it correctly adds/removes them from the standard Android bookmark database on the device.
Now to the problem. The Samsung browser looks like it has another internal bookmark database which maps the standard bookmarks to these folders - and this is what the browser uses. Bookmarks are stored by default in a HOME folder.
Now when PhoneMarks adds/removes bookmarks it doesn't update the Samsung bookmark (folder) database and hence it thinks that these bookmarks are not stored in a folder and hence doesn't display them. On the other hand they do appear in the 'last viewed' (and stared) as this list uses the standard Android bookmark database.
I will try and contact Samsung directly and ask the question of how to access this internal system and add bookmarks to a folder. Will keep you posted on my progress.
A way this problem could be solve would be to use the standard 'add bookmark' prompt dialog system during synchronising. This would mean that on first synchronisation you would be prompted to add every bookmark, but once done would only be prompted for new bookmarks. (This will probably only work in the Pro Version as it contains analysis code on which bookmarks have changed since last synchronisation).
So please bare with me on this issue and I'll keep you posted.