I've made a jsfiddle to illustrate my problem: https://jsfiddle.net/nickcoutsos/xzfoc8a9/41/
The description follows, but to use it quickly just click the big red Render button in the top right corner.
Here's the steps to reproduce:
shadowMap.enabled = true{transparency: true, opacity: 0.5}At this point the object looks... less transparent... brighter?
Here are my first and second renders respectively in case others can't reproduce the issue from the fiddle.

I'm not sure if it's that the buffer isn't being cleared properly or what, but there are couple of things I've found that ensure it doesn't happen:
In the latter case it's the transparent flag itself that matters and not just opacity === 1. I just discovered this yesterday so I haven't had a lot of different cases to test.
I've also tried:
renderer.autoClear = truerenderer.clear() before renderingforceClear argument when renderingIntel Iris Graphics 6100
Many thanks for reporting the issue and the fine test case! There was actually a bug in WebGLShadowMap. The linked fix should solve the problem.
You're a hero! I'm going to pull your branch and try that out tonight, thanks!
Most helpful comment
You're a hero! I'm going to pull your branch and try that out tonight, thanks!