I know other people have had the same problem so I am posting my fix for this. I have modified qpopper to place the .pop and .cache files in the user's home directory when home-dir-mail is defined. Use at your own risk.
#diff qpopper4.0.5.patched/popper/genpath.c qpopper4.0.5.patched/popper/genpath.c 136,139c136 < if ( p->pHome_dir_mail != NULL ) < len1 = strlcpy( pszDrop, pw->pw_dir, iDropLen ); < else < len1 = strlcpy ( pszDrop, p->pCfg_temp_dir, iDropLen ); --- > len1 = strlcpy ( pszDrop, p->pCfg_temp_dir, iDropLen ); 149,152c146 < if ( p->pHome_dir_mail != NULL ) < len1 = strlcpy( pszDrop, pw->pw_dir, iDropLen ); < else < len1 = strlcpy ( pszDrop, p->pCfg_cache_dir, iDropLen ); --- > len1 = strlcpy ( pszDrop, p->pCfg_cache_dir, iDropLen ); # Brad