Your mail folder (subdirectory) contains configuration data but not any email messages. Email messages are contained within the *.pmm folder files and companion *.pmi index files if stored in messages folders. If they are still "new mail" the messages are in *.cnm new mail files. In a default install your home mail box would be c:\pmail\mail\<username> or the default c:\pmail\mail\admin location.
In WinPMail do Help menu, About... and hit the Info button to see where your install shows your home mail box location and your new mail location. Search those locations for *.pmm and *.pmi and for any *.cnm files and report back what you find. At the least you will need to copy all *.pmm and *.pmi files and *.cnm files from the old location to the new location making sure none of the files are marked read only by the OS system. If they are you will need to remove the read only attributes because Pegasus Mail can not work with read only attribute message files. Many backup programs and cdroms mark files as read only.