It's probably not of much help, but for a short time I ran two elog daemons on the same linux box, using different ports.  It was thus able to run with two separate elogd.cfg files.   This is linux, and heavily biased to my eccentric way of running this linux box, but started them as:

/usr/local/sbin/elogd -p 8080 -c /home/logbooks1/elogd1.cfg -d /home/logbooks1

/usr/local/sbin/elogd -p 8081 -c /home/logbooks2/elogd2.cfg -d /home/logbooks2

Do note that as I was the only user on that linux box, I didn't have login etc.

However, I was soon asked questions by Andreas as to how I found this running, as he had encountered problems with an earlier version.  To be honest, that stopped me experimenting too far with this at that point, as well as a coincidental upgrading of my hardware.

But I was doing this *not* because I had to run two separate elogd.cfg files, but other reasons which meant splitting into two at that time vastly improved the performance of elog on the linux box at that time.  So while I didn't actually enounter any problems in doing so, I only have limited experience - and, of course, absolutely none on running even one [windows equivalent of a daemon] on Windows.

I am assuming here you have good reason for two separate elogd.cfg files, rather than just wanting to run two separate logbooks - guessing here, but one set public (no login) and one set private (with login)?