Sorry to hear you're having a problem with the Santa Fe, but I think once its working properly youre going to love it. I have the Castile insert, and when mine was installed they had to adjust a screw on the control unit to get the proper flame. Once that was adjusted they put the feed rod all the way in, for the slowest feed and lowest fire. Then the feed rod was moved out about 1/2 inch or so and that gave a nice sized flame, but later on I put the feed rod back in all the way to slow it down, and give me a smaller flame. Most of the time my insert is on the Low setting, and my flame on Low rises up over the edge of the firepot by about 3 inches most of the time, and then it will drop back to just a glow like yours for a minute or so until more pellets drop in then it goes up again. This is normal accorcing to the dealer.
Another thing, is when a Quad starts up it starts up on the High setting, no matter where you set the rocker switch at, and it will run on High for 4 minutes, this is normal, then it will drop back to whatever you have your switch set at. I leave mine on Low most of the time unless it gets down to 20 degrees or below in real cold weather then I usually kick it up to Medium if I need more heat. I found that for my living area I never have to set it on High, but I have run it on High for a couple minutes just to take the chill off the room faster. In 3 years of running mostly on the Low setting I never had any creosote problems as some people complain about here from running a low fire for a long time. I kick it up for a few minutes every now and then and its fine.
Quad stoves and inserts are very simple to run, they have no draft settings its all done automatically. It has a feed rate rod you can adjust, and a 3 position rocker switch for Low Med, or High settiing, the room blower speed is also determined by the rocker switch setting as well, so the Quads are fairly simple, there are not complicated adjustments to make. I will also give you a cleaning tip that the dealer gave to me. When you go to vacuum up your ashes and brush around in your firebox, before you do that click your stove on, and immediately click it off, before it has time to dump any pellets, this will allow your combustion blower to run while your inside cleaning, and willl suck any ash dust you make or stir up out and up the vent so you wont end up with ash dust in your living room. I find it very helpful, and that blower will run for about 14 minutes or so and turn itself off. You can then turn your stove on and enjoy.
Good luck, let us know what they find out....