Field settings form error: 'The selected selection handler is broken.'

I updated ctools from rc1 to rc2 and entity_reference from beta5 to rc1. My entity reference fields don't work anymore. If I go to the field settings, it says:

The selected selection handler is broken.

instead of the bundle selection form element. If I change the target type, it doesn't work better and I get this error in the watchdog:

Illegal choice 'base' in 'Entity selection mode'.

I tried to find the source of this problem. Here's what happens in function _entityreference_field_settings_process:
line 382: $handlers = ctools_get_plugins('entityreference', 'selection'); returns an empty array, and I guess it shouldn't.