From a quick reading it looks like homogenization may make fatty acids more accessible to lipase (greater accessible surface area, maybe also charge interactions?). Of course enzyme activity is also a function of pH and temperature. If it was a chilled storage tank, perhaps the taste was different because lipase had not yet had a chance to work--if homogenization happens before pastuerization, it could cause some breakdown after storage but before heat-moderated lipase inactivation.

I have some formal training in biology, but I'm certainly no expert and may be incorrect. What I do know is that dairy systems are complicated.