I use pine for my root acount (system mail) and it keeps one message in the /var/spool/mail/root file which says not to delete as it hold configuration for the mail folder. However, when I log in as root again It says I have meail when I don't, I just have that message in the mail forlder that say not to delete!!!!
Mailx checks for mail by looking at the time stamp on the incoming mail folder. If you wish consistent behavior, then you will need to use a single mailer consistently. There's no (easy) way to resolve the conflicting behaviors of pine and mailx.