Please take a look at the following information to try to troubleshoot this issue:
1. Set Options > Audio Setup > Processing > Dropout Protection to Maximum. Please read up on DropOut Protection in the Studio One Reference Manual.
2. If you open the performance monitor in Studio One, you can view the resources that are being used by each of your plug-ins. See if you can find a particular plug-in or set of plug-ins that might be causing the issue. On one of the songs that you are having high CPU usage, please open the performance monitor, press "Show Devices," expand it so it shows as much info that will fit on the screen, make a screenshot of this.
Please send the screenshot to Technical Support.
Here is a link to create a ticket: http://support.presonus.com/hc/en-us/requests/new