In this case I suggest to re-install update using MFG Tool:
http://ereader-store.de/DATA/N96ML/N...625f3_user.zip
MFG Tool works on Windows PC only. It must not be installed. Just download the package, unzip it in a folder. Connect your device to your PC (don’t use USB 3.0 ports) and start MfgTool2.exe from unzipped folder
You must set your Boox in download mode now. In order to do it re-boot your device in this mode using a special buttons combination:
1. Power off your device (long press of power button)
2. Press PgDn (<) + PgUp (>) + power button for 4 seconds. The led blinks once but screen remains unchanged. Your device is in download mode now.
MFG program window should report HID compliant device connected.
Press start button and wait for your update being installed
When after update the problem with the stylus persists, most likely it is something wrong with the stylus and it must be replaced.