The latest version of Pixelmator includes some improvements for stability issues with Pixelmator on certain 2011 Macs that have Intel HD 3000 graphics cards and OS X 10.11 El Capitan preinstalled.
Thanks to the fix, the app works again on these Macs. Unfortunately there is bad news for all other users, the bugfix made the photo editing application slower. Good news, you can disable the bugfix using the following Terminal command.