Binding of Isaac: Rebirth freezes when an overlay object disappears

The game Binding of Isaac: Rebirth freezes (not always, but almost always) whenever an overlay object (for example battery notification, notifications when adjusting screen brightness or sound volume, or Steam popups about achievements or friends) disappears from the screen. I then have to Alt+Tab out and force close the game.

I have tried reinstalling Steam, upgrading to new kernel, and installing new grapics drivers from oibaf repository. See thread here https://ubuntu-mate.community/t/system-notifications-freeze-binding-of-isaac/9198

I do not have this problem on my likewise Ubuntu MATE 16.04 x64 desktop computer.

steam version is 1:1.0.0.48-1ubuntu3

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: steam:i386 1:1.0.0.48-1ubuntu3
Uname: Linux 4.7.0-040700-generic x86_64
ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
CurrentDesktop: MATE
Date: Sat Oct 1 16:36:52 2016
InstallationDate: Installed on 2016-06-07 (115 days ago)
InstallationMedia: Ubuntu-MATE 16.04 LTS "Xenial Xerus" - Release amd64 (20160420.1)
PackageArchitecture: i386
SourcePackage: steam
UpgradeStatus: No upgrade log present (probably fresh install)