In regard to any suggestions, I would need more details.
For instance, is the angle of incidence for the angled joints the same for the straight joints? Is there any post clean up on the edges of the parts? Are all mating edges flat and relatively smooth? Is there any gap between the mating pieces? On a flat surface you won't have as much reflection so your beam will theoretically absorb better. You may be experiencing problems due to increased reflections created by the angled walls. However,at least with CO2 lasers, most porosity problems derive from either focusability or contamination (usually due to an oxide coating on the cut). If you have more details I would be interested to hear them. Hope this helps some.
Chad