Version 1.2.0+git20140201+r710~8173248+3~ubuntu13.10.1 from Ubuntu PPA. Reproducible: Always Steps to Reproduce: 1. Open Homerun. 2. Close Homerun. Actual Results: There is some visible "stuttering" and flickering when Homerun is closed, which is ugly. It fades slowly for a bit and then suddenly "pops" into invisibility. Especially apparent when opening and then closing Homerun repeatedly and rapidly. Opening isn't quite smooth either, but not as bad by far. Expected Results: Homerun fades in and out smoothly.
Well, I've tried on a different computer now, and there are no problems. Might have been the GPU drivers after all...
One reason might be whether you're using the Blur effect or not. The Blur and Fade effects interact badly due to a cache bug in the Blur effect: https://bugs.kde.org/show_bug.cgi?id=307112 All of this is outside of and can't be affected by Homerun, though.
I'm now using a theme that mostly eliminates transparency (so no blur effect), and Homerun is fading perfectly. In conclusion, it's probably what you're mentioning. *** This bug has been marked as a duplicate of bug 307112 ***