From what I'm reading above I think I'm having issues with my 5DMK3 and 600EX-RT.
When using Av/Tv modes the camera chooses settings without taking into account the flash (flash is set to ETTL mode). At first I wondered why my shots were blurry then looked at the exif data and the shots were taken @ 1/8th
I need to do some more testing but is anyone else experiencing this?
I think you can stop testing. There is no 'issue' here, other than user error. What you state is normal in Av mode - exposure metering ignores the flash because the intent is to expose the ambient (background) properly, then your flash fires a pre-flash which determines the flash power needed to properly illuminate the subject (ETTL). If you want a faster shutter speed, in the flash control menu you can set the shutter speed in Av mode to 1/200-1/60 s or 1/200 s fixed (instead of the default, which is Auto). See p. 192 of your manual, or p. 363 where this exact 'problem' is addressed in the troubleshooting guide. Changing that setting to a faster shutter speed will mean more of the light will be coming from the flash, which means the background will be underexposed, etc.)
Note, you state this occurs in Av/Tv mode - if you're getting 1/8 s exposures in Tv mode without setting that shutter speed yourself (which is the point of Tv mode - you, not the camera, are setting the shutter speed), you do indeed have an issue.