Particles interacting with semi-transparent matte objects cannot be rendered using a single output image, hence why your render looks odd.
Matte objects in Krakatoa define regions where particles should not be drawn, such that a Krakatoa render can be composited “over” the geometry pass (ie. from Default Scanline, Mental Ray, etc.). In the case of semi-transparent matte objects, the Krakatoa particles that are behind the matte objects must be composited “under” the geometry pass.
This is an important distinction because it is impossible for Krakatoa to generate a single image that can be composited “over” AND “under” another image. These are two separate operations, and Krakatoa supports this situation by allowing two separate images to be generated. There is a checkbutton in the Matte Objects Rollout called >Save Multiple Layers that enables this. When enabled, Krakatoa will save the usual “over” render (ex. myfilename_0000.exr) as well as the “under” render (ex. myfilename_layer1_0000.exr).
In conclusion, you are seeing 50% opaque matte objects rendering as 100% opaque matte objects because the particles behind the matte geometry are being rendered to the “under” buffer, which is not displayed in the VFB.
P.S. This technique is currently limited to 2 layers, which will only work if there is one layer of semi-transparent geometry. You can construct a case where there are particles in front of a semi-transparent plane, behind it but in front of another semi-transparent plane, and finally particles behind both planes. This situation will fail because it require three layers of particle renders. Most geometry renderers will only output one image anyways, so it doesn’t really matter what Krakatoa does since it cannot be composited between the geometry without multiple geometry layers.