ReeceZ,
From your description it sounds like you may have a frayed wire to a sail switch (switches at the ends of each hydraulic ram that signal the ram is at full extension or fully retracted), or a corroded/bad connection. The tonneau cover striking the folded top jars the connection completing the circuit?
If you think this may be the case, download the FSM from this site and research where to look for the wiring to the sail switches. You may have to remove the inner top lining to get at some of them, and that is in the FSM as well.
I'm not certain this is your issue, but its a good place to start, as others here have found frayed wires in the folding top mechanism and correcting them has cured their top problem. Good Luck!
Gene
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