Mosty the reason for this is: antivirus software. It started to scan the file before JD receives acknowledge from the server that everything is transmitted correctly. Since the AV has to check inside the archive (unpacking it somewhere in the TEMP directory) it can consume a lot of CPU usage (beacuse AV should work quick as possible) and other processes may suffer.
The best policy is to search if your AV/FW software has the rules for not scanning network traffic from jdownloader/java/javaw executables.
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