Are multiple files (running in parallel, using Parallel Computing Toolbox or some other mechanism) trying to modify the preferences or the settings simultaneously? If so we're going to need to see those files and know more about how you run them in parallel to be able to suggest how to avoid the file contention. If you don't feel comfortable posting that code on MATLAB Answers you could contact Technical Support directly using this link and ask them to help you determine what's causing the contention and how to avoid it.
You also said "As a consequence, one of the sensors can stop to collect data, i.e., I can not read correctly form a specific serial port, and in the next time I run the same matlab script," after an error. What is the full and exact text of that error message (all the text displayed in red in the Command Window)? If there are any warning messages (displayed in orange) please show those as well.
