Sorry for the delayed response: I didn’t have the file available over the weekend.
When preparing your request based on a slightly different file I noticed a repetition in the issue; It seems that the component had problems with some situations of solids were an edge is shared. The goal of the union at this point in the process was to make 1 solid of all involved solids, and some solids had (only) an edge joined.
I remember I have had similar problems in Rhino. Solids that are only touching via an edge can not be unioned.
I guess the fail was a result of the order in which the joining was taking place. If intersecting solids were joined first, one edge was eliminated and therefor posing no problem for further joining with solids that shared that edge, as it wasn’t shared anymore. This obscured the problem.
The problems seems solved by altering the solids a bit: by making sure no edges that are falling inside a larger solid (and therefor have no effect on the actual result) are in the same position, the union is succesfull.
Thank you for pointing in the right direction!