I have solved the problem!
The instructions are a little complicated, so make sure you follow them exactly.
First of all, I have tested these instructions and they definitely work. Sorry about the faulty ones I accidentally posted before.
Second of all, the file that you have to edit is /etc/xdg/menus/lxde-pi-applications.menu
, not /home/pi/.config/menus/lxde-pi-applications.menu
Open the file and scroll down to the section that looks like this (around line 137):
<!-- Other -->
<Menu>
<Name>Other</Name>
<Directory>lxde-other.directory</Directory>
<OnlyUnallocated/>
<Include>
<And>
<Not><Category>Core</Category></Not>
<Not><Category>Settings</Category></Not>
<Not><Category>Screensaver</Category></Not>
</And>
</Include>
</Menu> <!-- End Other -->
Change it to look like this:
<!-- Other -->
<Menu>
<Name>Other</Name>
<Directory>lxde-other.directory</Directory>
<OnlyUnallocated/>
<Include>
<And>
<Not><Category>Core</Category></Not>
<Not><Category>Settings</Category></Not>
<Not><Category>Screensaver</Category></Not>
<Not><Category>X-Debian</Category></Not>
<Not><Category>X-Debian-Applications</Category></Not>
<Not><Category>X-Debian-Applications-Accessibility</Category></Not>
<Not><Category>X-Debian-Applications-Editors</Category></Not>
<Not><Category>X-Debian-Applications-Education</Category></Not>
<Not><Category>X-Debian-Applications-File-Management</Category></Not>
<Not><Category>X-Debian-Applications-Graphics</Category></Not>
<Not><Category>X-Debian-Applications-Network</Category></Not>
<Not><Category>X-Debian-Applications-Network-Communication</Category></Not>
<Not><Category>X-Debian-Applications-Network-Web-Browsing</Category></Not>
<Not><Category>X-Debian-Applications-Programming</Category></Not>
<Not><Category>X-Debian-Applications-Science</Category></Not>
<Not><Category>X-Debian-Applications-Science-Mathematics</Category></Not>
<Not><Category>X-Debian-Applications-Shells</Category></Not>
<Not><Category>X-Debian-Applications-Sound</Category></Not>
<Not><Category>X-Debian-Applications-System</Category></Not>
<Not><Category>X-Debian-Applications-System-Administration</Category></Not>
<Not><Category>X-Debian-Applications-System-Hardware</Category></Not>
<Not><Category>X-Debian-Applications-System-Monitoring</Category></Not>
<Not><Category>X-Debian-Applications-System-Package-Management</Category></Not>
<Not><Category>X-Debian-Applications-Terminal-Emulators</Category></Not>
<Not><Category>X-Debian-Applications-Video</Category></Not>
<Not><Category>X-Debian-Applications-Viewers</Category></Not>
<Not><Category>X-Debian-Education</Category></Not>
<Not><Category>X-Debian-Games</Category></Not>
<Not><Category>X-Debian-Games-Adventure</Category></Not>
<Not><Category>X-Debian-Games-Toys</Category></Not>
<Not><Category>X-Debian-Help</Category></Not>
<Not><Category>X-Debian-Screen</Category></Not>
<Not><Category>X-Debian-Screen-Locking</Category></Not>
<Not><Category>X-Debian-Screen-Saving</Category></Not>
</And>
</Include>
</Menu> <!-- End Other -->
A restart may be required for the changes to take effect.
This worked for me and should solve the problem.