Of course, perception is not always supported by research...
"Milk and dairy product intake was not associated with an increase in upper or lower respiratory tract symptoms of congestion or nasal secretion weight. [...] We conclude that no statistically significant overall association can be detected between milk and dairy product intake and symptoms of mucus production in healthy adults, either asymptomatic or symptomatic, with rhinovirus infection." [link]However, other research support the possibility that dairy products might increase mucus production only if the milk contains beta-CM-7 protein (not all milk contains this protein). [link]
I have a different hypothesis for why milk may cause the perception of increased mucus production. I should preface that I have no research study to quote to prove this hypothesis. Might be a good research project for a medical student???
In any case, milk contains a protein called casein. When the milk is not refrigerated, it causes bacteria to metabolize lactose within the milk leading to lactic acid production as a byproduct. When acidity is present, the casein congregate in a process called curdling. That's the "chunks of milk" seen in milk gone bad.
Now, bacteria certainly will not be playing a role in lactic acid production after fresh milk is consumed, BUT, there IS acid present in the stomach which can initiate curdling.
Now what if a patient suffers from acid reflux... and what if some of the reflux episodes reach the throat level?
So, hypothetically speaking, if somebody who suffers from acid reflux drinks a lot of milk, two things might hypothetically happen (or drinks orange juice followed by milk):
1) Milk temperature goes up from body heat (which assists in curdling)
2) Acid present from the reflux will initiate curdling
If acid is present in the mouth and throat from reflux or secondary source (like recently drunk orange juice), curdling to some degree may occur from milk residue mixing with acid residue present leading to perception of mucus production.
Now does this actually happen???
I don't know and I hope some researcher looks into this hypothesis further!
However, in the end, if dairy avoidance helps with a phlegmy throat, than it can't hurt to avoid it! I should also point out that egg and wheat does cause a similar phlegmy problem in some patients.
Relationship between milk intake and mucus production in adult volunteers challenged with rhinovirus-2. Am Rev Respir Dis. 1990 Feb;141(2):352-6.
Does milk increase mucus production? Med Hypotheses. 2010 Apr;74(4):732-4. doi: 10.1016/j.mehy.2009.10.044. Epub 2009 Nov 25.