/etc/log.d/conf/logfiles/exim.conf has the logfile of /var/log/exim/main.log,
this should be exim/main.log.

/etc/log.d/conf/logfiles/pureftp.conf has the logfile of
/var/log/pureftp/syslog.log, this should be pureftp/syslog.log.

Below is the strace output showing what the logwatch scripts try to open. 
/u3f2/log is where I am storing my logs.  Log files that are under /var/log
should have relative paths.  For the case of log files such as
/var/spool/autorpm/install.log the correct thing to do would be to not pre-pend
directories to absolute paths.

Finally /var/log and /var/adm should not be searched unconditionally.  There
should be a config variable containing an array of directories to be searched in
order, "/var/log" would be the default for such an array, but the sys-admin
should be free to add others as necessary.

/root/str.29762:stat64("/u3f2/log//var/log/pureftp/syslog.log", 0x81ac0c8) = -1
ENOENT (No such file or directory)
/root/str.29762:stat64("/var/adm//var/log/pureftp/syslog.log", 0x81ac0c8) = -1
ENOENT (No such file or directory)
/root/str.29762:stat64("/var/log//var/log/pureftp/syslog.log", 0x81ac0c8) = -1
ENOENT (No such file or directory)
/root/str.29811:execve("/bin/sh", ["sh", "-c", "/bin/cat
/var/log/pureftp/syslog"...], [/* 28 vars */]) = 0
/root/str.29812:execve("/bin/cat", ["/bin/cat", "/var/log/pureftp/syslog.log"],
[/* 28 vars */])                                = 0
/root/str.29812:open("/var/log/pureftp/syslog.log", O_RDONLY|O_LARGEFILE) = -1
ENOENT (No such file or directory)
/root/str.29812:write(2, "/var/log/pureftp/syslog.log", 27) = 27