I faced with a very annoying bug, sometimes IDEA shows me an empty transparent windows:
I can't determined what causes this bug. I have to recall dialog to see the content inside window
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I have a similar problem, but do not know the cause. "Occasionally" windows or dialogs of various apps come up with totally transparent content, or full screen apps have app name in top bar, but the rest of screen is totally transparent just showing the background. Totally closing and reopening the transparent dialog or app restores it to completely visible. I don't think I have anything set to be transparent, and cannot find any setting for that.
It occasionally happens with nvidia-375 or nvidia-378 with GTX 750 Ti or GTX 1060. But I am running stock 64-bit Ubuntu 16.10 because 16.04 seemed to blank all text during even cold boot (BIOS splash and grub menu totally black) until something (gui login or Win7) displays graphics. 16.04 boots fine on other older/newer computers, but I have not run them long enough to see if they exhibit the rare window transparency issue.
I did find a setting in CompizConfigSettingsManager that defaulted to screen refresh rate 50 and I changed that to its actual 60. But I will have to wait to see if random window transparency still happens.