Many clumpy liquids can be saved with a hand-held blender or high powered blender or even a food processor {although not a food processor if liquid is too liquidy.} Were you making a roux? Non-homogenized milk will act as homogonized milk, even if it comes to a boil, although if it was raw it can sometimes turn {begin to go off}, thus becoming acidic, and acidic dairy has a hard time staying together {emulsifying} when heat is applied.

I like to start my roux with a whisk and one of my tricks is to always whisk "tight" from the center out, as I would a ganache, to keep lumps from occurring. this sort of "trick" is especially helpful in making pastry cream, which is really just a high fat roux.

does this help? hope so!

We've done a little research into homogenization and it does seem that your hunch would be correct. Are you using raw milk? Was it at a rolling boil and how did you incorporate your flour? Heat can cause the fat to separate from the liquid, and my guess is that since you were already using unhomogenized milk, boiling didn't its already precarious suspension.