This was reported to the support team, but in the meantime I decided to redo a couple of spaces to see what is happening. I have removed and redrawn spaces and visually have made sure, by zooming in to the microscopic level, that there are no intersections whatsoever at the sample spaces. I have ran the rebuild function, ran the model report and voila, they still show up in the report as intersected spaces. I check the spaces visually only to find that IES has actually caused these spaces to intersect! I have attached a picture to this post to make it more visual.
Conclusion: Rebuild Model Adjacencies function in some cases, with no known reason, can cause spaces to intersect.
This is a huge pain in the arse and waste of valuable project time, which needs to be addressed as soon as possible.


