There are many issues with serial communications. Very often it's just a connection problem, with faulty cables/connectors. Other issues may arise from poorly implemented exchange protocols between instrument and PC, synchronization being a classical problem.
Try to post a version of your vi. Some "expert" here will be able to detect a flaw into your code, if any.
Otherwise I'm afraid that nobody will be able to help you efficiently.
CC
Chilly Charly (aka CC)
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