I doubt it has anything to do with what you add to the water. I have run mine with plain water as well as with nutrients etc.

Are the cuttings getting constant moisture?
Are the stems getting crushed by the inserts?

too much sun/heat can be an issue and wilt the cuttings.

Cutting are constantly sprayed.
Some stems were a little large but i spread the neopreme inserts so they would not be crushed.
Flourecent light is 3 ft above cloner.
Chiller is set for 70

First batch just got slimey and rotted.

Second batch seemed to be an issue at insert but it happened fast and may have had PH way to low do to test kit range.

When I start seeds under Flourecents I only leave 6" or less spacing from light, otherwise it's not enough light. I imagine cuttings would be the same.

I have had cuttings rot before they rooted before - but usually that takes a month. Salvia's are generally very easy.
I insert mine as far as they will go - up to touching the bottom of the net-pot. I have used Olivia's rooting gel, which seems to seal the stem from drying - at least until it washes off...

Not sure what a chiller is, some type of cooler ?

chiller is a cooler
most have rotted again on 3rd batch.
here r some pics from 2nd batch
[IMG]http://i6.photobucket.com/albums/y226/skidbump/P1010004-1.jpg[/IMG]
[IMG]http://i6.photobucket.com/albums/y226/skidbump/P1010003.jpg[/IMG]
[IMG]http://i6.photobucket.com/albums/y226/skidbump/P1010001.jpg[/IMG]

pics from 3rd "last batch after 9 days

[IMG]http://i6.photobucket.com/albums/y226/skidbump/P1010015.jpg[/IMG]
[IMG]http://i6.photobucket.com/albums/y226/skidbump/P1010005.jpg[/IMG]

[IMG]http://i6.photobucket.com/albums/y226/skidbump/P1010013.jpg[/IMG]

One of two things. There's too much moisture or you're not keeping the cuttings clean. I've had that same problem with my homemade machine. I finally set my timer to run 30 minutes and off for 1 hour. It's made a great deal of difference in how many cuttings I lose to rot.

At first, I was having great success. Now, I get about 1/2 my cuttings to root. Maybe it's what I'm trying. Salvias almost always rot before they root for me. The hollow stem allows water inside and they turn black in days.

You need to completely sterilize your cloner JUST before each use.

Take each sprayer off of the manifold. Fill cloner with water and ONE cup bleach and run for 20 minutes.

Clean each sprayer with a nail or piece of wire. Make sure to remove all material.

Replace spayers on manifold and run another 20 minutes. During this time I flip the neoprene a few times.

Toss bleach water rinse and fill with tap water, run for 20 minutes flipping neoprene once.

Toss fresh water, refill and use right away.

Dutch Masters Zone should be added if water temps are above 70f.

This will get you back to a 100% strike rate in a matter of days.

This is in the instructions that came with your cloner.
Have fun!

Besides the moisture issues, it may also be your cuttings. The PDF instructions you linked to did not describe about how the cuttings should be (and understandably, it can't predict what plant you are taking cuttings from).

I myself did many cuttings above a leaf node, and would bury the cutting with that single stem into the ground.

Even for easy plants, people kept saying that in 7-10 days, the plant will root, but I kept the cuttings going for 14-28 days or more and nothing.

Only recently have I realized that for some plants, cuttings should be below a leaf node, and then this part should be buried.

For those plants, It is in this area that roots will grow. Once I corrected that, even on the very same cuttings that I had been trying to root for over a month (making a 4-inch cutting become 2-inch so that I could just take the part that included cutting below the node), then I began getting much more rooting, even with those short cuttings.

Some plants do root in different ways. An example might be your bushes that you had 90% success with. By using that cutting, you stopped the flow to the root system, which is similar to what air layering does, and the cutting triggered a response to start making roots at that point, without the cut being related to a leaf node.

Hope that can help you if that is something that was different about your salvia cuttings and your bush cuttings.