It is simplistic (wrong) to believe that it is just a 'bad habit'. There is an actual 'neurological' disorder which makes uttering some sounds (often consonants) or transition from one sound (syllable) to another difficult. When the nerve impulse for the next syllable fails to come from the brain, the speech system repeats the last sound, until it arrives. Sometimes no sound or air may escape- a block. PWS often describe it as locking up of their jaw, tongue or mouth. This leads to
considerable struggle behavior- as if we are trying to force the word out of our mouths. Eye blinking, grimace, head nodding or movements of other parts of body may be associated with this
struggle. At one time, we may have used it to get out of this 'block', and then they become unconscious secondary behavior.

Brain scan studies have found no differences in brains of PWS when they are not talking, and when they are talking fluently. But during stuttering, changes are seen in their brain activity. Left-brain areas (where speech and language are produced) which should be active during speech, become inactive, while right-brain areas which should be inactive during speech, become active. Unusual right-hemisphere activity is related to fears, anxieties, or other emotions PWS may
associate with speech. So it can not be said if this is the cause or the effect of stammer.

Brain scans have found abnormally low activity during stuttering in the central auditory processing area, and in the area that integrates auditory and somatic (body) sensation. Stuttering seems to be related to an inability to integrate what the PWS hear - with the muscle movements they feel.

Stuttering appears to be caused by excessive amounts of the neurotransmitter dopamine in the left caudate nucleus. This is the area that translates speech into muscle movements.

Another prominent view is that stuttering is caused by neural synchronization problems in the brain. Recent research indicates that stuttering may be correlated with disrupted fibers between the speech area and language planning area, both of which are located in the left hemisphere of the brain. Such a disruption could potentially be due to early brain damage or to a genetic defect.

Stress & Anxiety: In certain situations, such as talking on the telephone, stuttering might increase, or it might decrease, depending on the anxiety level connected with that activity. Stuttering appears to reduce stress in PWS temporarily, as measured by systolic blood pressure, but then causes stress, creating a cyclical pattern in which the PWS stutters on the first syllable of the first word, then says the rest of the word and several more words fluently, then stutters again, then says a few more words fluently, and so on.

One study found that developmental stuttering and Tourette Syndrome may be pathogenetically related. The central feature of Tourette syndrome is 'tics'; Tics are repetitive, semi-voluntary movements such as eye blinking, throat clearing, coughing, neck stretching, and shoulder shrugging, etc. Tics are exacerbated by stress, and when the affected person tries harder to control the undesired movement, the conditions can become more pronounced. But while Tourette's is considered a health disorder, stammer is thought of as a 'strange habit'.

From the research of Per Alm, another theory is that there are two  pathways in the brain, responsible for speech. While the medial path deals with spontaneous speaking, the lateral path deals with speech, where 'timing cues' are coming from outside like reading in unison, singing, talking to the rhythm of a metronome etc. It is proposed that the medial path is affected among the PWS; therefore spontaneous speech may be affected but singing, reading in a group etc. might be quite normal. Further, the lateral path has the ability to provide timing of speech without external cues, but it requires greater conscious focus on certain aspects of speech. For example, PWS may stutter much less, while imitating a dialect, an accent, doing role play, whispering etc.