Sure wish I could get this fixed.
Have you tried a complete new install to a different directory entirely to rule out problems with the OS. If this works then you can point at the folders in the old mail directory to get your data. You can then copy the PND files for the old directory to the new to get the POP3 and SMTP setups. If all of this works normally then I suspect that there is some sort of problem with your state.pmj, pmail.ini or folstate files that are causing the problem.
You can then delete (rename) the pmail.ini, state.pmj and folstate.pm files in the original system and it will allow you to start as new without losing any data at all. You will have to use the POP3/SMTP setup and reselect the POP3/SMTP setup and rebuild manuall any identities you were using.