Hi Valky,
My pen often does stop responding but not after plugging the DR1000S in like you described. My pen stops working after the reader wakes up from sleep mode.
I usually find navigating to Settings|Personal Preferences, switching the stylus off, selecting "Save & Close" and then switching the stylus on again will fix this problem. Unfortunately if you have switched the buttons off there is no way to navigate so a reset is the only option.
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