TL;DR Try P mode on the camera.

You need to learn how flash works. Putting everything on auto is the easiest way to lose control over exposure with flash. If you're shooting in completely consistent circumstances all the time (which seems likely), you'll probably do better having everything on M mode, finding out what works best, and then locking down the settings.

The auto-exposure system in the dSLR has to make a decision about how you want to balance the flash illumination against the ambient (all the light that isn't from the flash) light. There is no single right choice here--you can do everything from all flash/no ambient to no flash/all ambient and everything in between. But the camera manufacturers have decided that most folks will be using A or S modes with flash for fill. So that is how the flash will behave on the auto modes: most of the light coming from the ambient, and only a small amount of flash to "fill in" the shadows. This is most typically used in a daylight portrait scenario.

The P (Programmable Auto) mode acts a little differently. The flash will behave as fill in well-lit situations, but in lower-light situations the behavior will then shift to using the flash as the main source of illumination--like a P&S built-in flash. This is more likely to be the easiest setting for any circumstances if you don't want to step in and take control of the flash and ambient exposures explicitly through the exposure values.

M mode on the camera allows you to completely control where you want to set the balance between the flash and the ambient. ISO and aperture affect both the ambient and the flash illumination. And shutter speed only affects the ambient (if you're below your max. sync speed), so you do have a control to independently adjust the balance (shutter speed. See: dragging the shutter on neilvn.com)

Flash is also controlled by two other things: the distance of the light from the subject (the farther away, the lower the light level gets), and the flash power setting. This is why most of us who are into lighting will use an off-camera flash (to be able to adjust placement and angle as well as add modifiers), and M mode on the flash for precision and consistency of the power setting.

TTL is metering-based. The camera tells the flash to send out a preflash burst of light of a known power/brightness level, meters it, and then adjusts the flash's power level to where the autoexposure system thinks is a good exposure. Like using the A or S modes on the camera, it is fast and convenient, but may not be exactly where you want the exposure to sit. Just as we use M mode on the camera for precision and consistency, we use M mode on the flash, too.

See: Neil van Niekerk's Flash Photography Techniques and the Strobist.