Does there seem to be any regular time frame that this occurs? Also, what version of firmware is currently running on the SoundStructures?
If there is a lot of feedback from the control device you could be running into memory overflow issues, do you currently have flow control turned on? If so I would recommend turning that off along with an upgrade to 1.5 firmware on the C16s (if that's not the currently running version. After upgrading to 1.5 ensure you use the latest SoundStructure Studio as well (version 1.7).