Hi Randy yeah so this kind of thing is a kind of difficult case to get an automatic tolerance mechanism to work very well with.

The overall object size is about 2.4 units across, so the relative tolerance mechanism looks at that bounding size and decides that a tolerance of 0.001 units would be a good tolerance for that.

But some of the individual cylinder fillets you've got in this piece have a radius of only 0.002 units - that's too close to the intersection tolerance and when the fitting tolerance is too close to the size of entire edges like you've got here it becomes easy for some things to glue entire edges to one side (since both sides of the whole edge are within tolerance of some other piece that it's intersecting or measuring against).

If you scale your object up by 10x in size, you'll have an object size of about 24 units across and the relative tolerance mechanism will still pick a fitting tolerance of 0.001 units for this (it uses that for anything between 1 and 100 units across), but now that fitting tolerance will be small enough in comparison to those individual features that accurate enough intersections will get generated.

Generally I'd recommend not creating things at too small of a scale like where individual edges or radius values are approaching very close to 0.001 units in size, instead try to scale such an object up by either 10 times or 100 times so that individual pieces are more like 0.01 units across or so instead of nearly 0.001 units across.

- Michael