I have an unlocked iPhone 5S purchased in the Netherlands. I use with T-Mobile in the NL and with AT&T in the U.S. Phone is at 7.04 release. More recently people I was talking to complained that my voice was muffled. I have associated with 7.04 but this may be a result of the noise cancellation setting being set to on as default with 7.04. (I came to this conclusion checking several 7.04 iPhones and finding noise cancellation turned on. This was on phones where the users had no idea that the feature even existed.)
The active noise canceling works by subtracting common sound levels detected by the rear microphone from the sound levels detected by the voice microphone. Normally the rear microphone hears background or ambient noise and the front microphone your voice + background noise. With noise cancellation turned on the background noise is subtracted and your voice is clearer to the person on the other end of the phone. For this to work correctly the rear microphone need to be UNOBSTRUCTED.
The muffled voice problem occurs when both microphones hear your voice. With a flip case such as the Book Book used in the folded back position the case routes enough of the voice to the rear microphone to "muffle" your voice. This is noted on the Twelve South webpage. I tested this and found that with the case folded back gave muffled voice, with it open no problem. Also no problem with the phone out of the case.
Covering the microphone with your finger fixes the problem in that it the rear microphone does not hear any sound and the front picks up your voice + background. As long as you are not in a noisy environment your voice will sound clear. This should be the same effect as disabling the feature (Settings / General / Accessibility / Phone Noise Cancellation).
If the problem still persists with noise cancellation turned off and you are in a reasonably quit environment when using the phone and still have the problem then a call to Apple support is a reasonable next step.