Just to be sure I fully understand your setup, you have a Futaba receiver, outputting SBUS to the Cortex and then you have the 5 Cortex outputs connected to five of the inputs to the SBE-1 and the SBE-1's SBUS output driving the SBUS network in a plane. When you say you see the glitching in the PC software, I assume you mean the Cortex PC software. If you see glitching there then the Cortex is having problems decoding the SBUS input and is probably passing the problems on to the SBE-1 and everything that follows. Here is what I would do first.

1) Connect the SBUS receiver output to the Cortex Sum Signal Input (next to setup jumper).
2) Connect the Cortex to the PC interface and first make sure the Cortex has the latest firmware.
3) Use the PC interface to ensure that the Cortex is configured to accept SBUS input and Analog servo outputs
4) Look at the Cortex outputs using the PC interface and verify that all the controls are operating the expected channels and everything works smoothly.
5) Connect some servos to the Cortex servo outputs and verify that they all operate smoothly,

If all of the is working correctly, disconnect the servos from the Cortex and connect the SBE-1. It should work properly at that point as it shouldn't be able to
tell the difference between a receivers servo outputs and the Cortex servo outputs..

Hope you're able to get it sorted out.