Hi Falk,
We tried to reproduce this issue with Essential version 5.1, but could not get this issue. Maybe I am not following the steps that you are doing. Attached sample hides "custom" option from the gridfilterbar dropdown. Please refer to the attached sample and its screenshot for more details.
Sample :
http://www.syncfusion.com/support/user/uploads/customize%20dropdownlist.zipScreenShot :
http://www.syncfusion.com/Support/user/uploads/GridFilterbarScreenShot_4b2f0d9c.zipPlease try to provide us some more information on this issue, this will help us to analyse the issue here and get back to you with the solution.
Thanks for your patience.
Best Regards,
Haneef