Yes looks like about 0.0004" TIR from where I'm viewing which is great. I've kind of lost track what exactly you are insertng & testing, but generally an ER collet itself should be about the same runout so I'd guess collectively you would be in the 0 - 0.001" clamping on a perfectly true dowel pin. So try that next, ideally on the same collet size you are using. If you part is measuring something substantially more than 0.001" its likely not circular/concentric. Now this holds true by positioning the DTI ball right close to edge of the collet. If you have a healthy part stickout & the part is cocked for whatever reason, it could measure runout because of that angle. If the collet was not quite tight enough or the part had a slight taper... Again, ER is better than other holding systems in this regard because it has more longidudenal contact area over its grip (as opposed to 5C which is more of a nose pinch). Only other thing I can think of is if your part is a hollow tube & tightning it in the collet manages to distort the wall thickness. This is typically a 3J or 4J chuck issue though. Again, ER is better here because it is a relatively radial grip force, meaning equal pressure through each of its leaves.
All you can do is add one step or part at a time & try & isolate it. But looks like you have eliminated the ER seat. Last question, you are snapping the collet into the end cap ring correctly each time before tigtening right? I dont even think it will work otherwise but just mentioning because some guys seem to have more stubborn rings.