I have 6D and 40D and couple of days a go I started to have a problem with low exposure when I'm working on ETTL with my Speedlite 600EX-RT. On manual it gives full power, i can adjust the flash output but theres no changes on the power.
I done reset at the flash, changed the batteries and all the same.
So, on eTTL it underexposes but on manual mode it only pops full power flashes? Are you using radio triggers or on-camera?
If that's the case either something is completely screwy with the electronics, or there are two different issues.
However, the first thing I would do is completely remove the flash from the camera, check the contacts - clean them with alcohol if necessary - and rettach. Firmly. Flashes can act oddly when not fully seated, and sometimes you can even lock the flash on when it's improperly seated.
For the eTTL underexposing I would first check the Flash Exposure Compensation. I would also do some controlled tests with the camera in full manual mode so I was seeing consistent results.
For the manual flash, hopefully it's just a seating issue. If not, the flash probably needs repair. But again, first thing I would do is some controlled tests to make sure it wasn't user error.
There was an issue with the 580ex where a transistor burnt out and cause a similar issue. I haven't heard of the same issue with the 600exRT, but you never know.
You may have adjusted the flash-exposure compensation (FEC) on the flash. This only affects ETTL because when using manual, the flash power is dialed in manually. But in E-TTL the camera and flash calculate the correct flash power automatically.... but then apply a flash exposure compensation adjustment.
It is actually possible to dial in flash-exposure compensation either directly on the flash OR on the camera. But if this is happening to BOTH your 6D and 40D then it's likely you dialed the change in on the flash.
To check, on your 600EX-RT, there are four soft-buttons just below the LCD display. The 2nd button, is uaully labeled "+/-" but as these are "soft buttons" it's possible to get to additional pages of menu settings. Press the "+/-" button and it should display the current flash exposure compensation value and you can also use the dial on the flash to increase or decrease compensation. Hit the SEL./SET button in the middle of the dial to enter the change.
Alternative you can press-and-hold both the 2nd and 3rd soft buttons on the flash simultaneously for about 3 seconds until the message "Cleared" appears on the bottom of the LCD screen and this will clear the flash settings (including exposure compensation.)
It is ALSO possible to change flash exposure compensation (FEC) on the camera itself... and if you do this the display on the flash will not show the adjustment. I think that's less likely because if both the 6D and 40D are a bit dim then you would have had to have adjusted each camera's FEC and it is unlikely that you would do it unintentionally. On the camera, the icon looks like a lightning bolt with a +/- next to it.
Flash exposure compensation is only applied when using E-TTL. When in manual mode the flash fires at whatever power level you set (e.g. 1/1, 1/2, 1/4 etc.)
Canon's approach to flash photography appears to be that blown foreground highlights are to be avoided at all cost, and their ETTL algorithm enforces that principle rather effectively. So if you photograph a person wearing a white shirt in a room with a deep, dark background with the camera set to a low ISO number, the shirt will be properly exposed but the rest of the scene will be dark. But if you expose for the dark background, treating the flash as fill, the algorithm will decrease the power of the flash to avoid blowing out the shirt, and the scene's overall lighting should be OK. All this takes some getting used to, but on the whole it works pretty well.
There are times, of course, when you can't expose for the background, because it's simply too dark. In such cases you may need to use a manual flash setting, choosing the power level so as to light the foreground sufficiently without blowing out the highlights. Often the best solution, if you're in a room that supports it, is to use bounce flash. Bounce flash reduces the contrast between foreground and background, and the ETTL algorithm handles it very well, at least in my experience. This is why, as I believe someone mentioned in a parallel thread, a picture taken with bounce flash often looks much brighter than the same picture taken with direct flash.
As for TTL, the Canon speedlight manuals will usually tell you not to use it on a camera designed for ETTL. The two methods are incompatible, and using TTL makes the flash fire at full power, resulting in gross overexposure. I've accidentally made that mistake once or twice, and the result wasn't pretty.