I changed my key bindings to match yours (s=throttle up, x=throttle down, p=pause) and tried toggling pause multiple times while using the default C4 jet. I was able to adjust my throttle up or down each time without issue.
Please provide additional, step by step details to recreate this. Which plane do you see this in? How many times do you have to press the pause key? Please include a copy of your log.txt from after one of the times you see this.