This is most likely related to a problem we have found related to the Pin Configurator.
Each time you open a pin configuration file and under the condition that the package view is visible, a number of resources get allocated (=> this also happens when you open a project).
The problem is that the allocated resources are not released properly as soon as a pin configuration file gets closed. This means that repeatedly opening and closing projects and / or pin configuration files will result in a 'no more handles' error.
This problem will be fixed in the final version of e2 studio v5.0.0, scheduled to be released towards the end of April, 2016.
(The e2 studio v5.0 you are currently using must be the Alpha version from the Gallery).