Just an update: I am still encountering similar performance issues with the 4.9.0-1 kernel that was recently promoted to testing. In fact, the 4.9.0-1 kernel may be the worst yet in terms of this specific issue, with IntelliJ starting so slowly as to be effectively unusable. One time the entire system appeared to become completely unresponsive & a hard reset was required.
The most recent kernel with which I've experienced problems:
$ apt-cache show linux-image-4.9.0-1-amd64
Package: linux-image-4.9.0-1-amd64
Source: linux-signed (4)
Version: 4.9.2-2
Installed-Size: 183299
This problem does not seem to occur with a vanilla 4.9.2 kernel, implying something Debian-specific:
$ uname -a
Linux desktop.local 4.9.2 #1 SMP Wed Jan 25 04:28:29 PST 2017 x86_64 GNU/Linux
If you're aware of any Debian patches that might be suspect, I'm happy to try some custom builds. Reproducing the issue is trivial on my end when a kernel is "bad".