I'm not sure if this has to do with new API changes, but is there a way to disable the slide up/down animation for panel popups? I prefer no animations, and always disable window animations, but it doesn't seem to be disabling popup animations.
Does disabling 'effect on menus' in effects tab help?
No it doesn't.
I see this in .xsession-errors when I toggle that option, though:
(cinnamon:2221): St-CRITICAL **: st_widget_get_theme_node called on the widget [0x561c13ce4ff0 StScrollView.popup-sub-menu] which is not in the stage.
Turning off "Effects on menus" in Cinnamon Settings->Effects should do exactly that. It does here.
I built Cinnamon from the git source a few days ago, then switched to the nightly PPA. Do these versions look current?
jason@jason-virtual-machine ~ $ dpkg -l | grep cinnamon
ii cinnamon 3.2.1-20161111040014-xenial amd64 Modern Linux desktop
ii cinnamon-common 3.2.1-20161111040014-xenial all Cinnamon desktop (Common data files)
ii cinnamon-control-center 3.2.0-20161111013030-xenial amd64 utilities to configure the Cinnamon desktop
ii cinnamon-control-center-data 3.2.0-20161111013030-xenial all configuration applets for Cinnamon - data files
ii cinnamon-control-center-dbg 3.2.0-20161111013030-xenial amd64 utilities to configure the Cinnamon desktop - debug symbols
ii cinnamon-desktop-data 3.2.0-20161111000245-xenial all Common files for Cinnamon desktop apps
ii cinnamon-doc 3.2.1-20161111040014-xenial all Cinnamon documentation
ii cinnamon-l10n 3.2.1-20161111040122-xenial all Translation files for the Cinnamon desktop
ii cinnamon-screensaver 3.2.0-20161111013004-xenial all Cinnamon screen saver and locker
ii cinnamon-screensaver-webkit-plugin 3.2.0-20161111013004-xenial all Webkit plugin for cinnamon-screensaver
ii cinnamon-screensaver-x-plugin 3.2.0-20161111013004-xenial all XScreensaver plugin for cinnamon-screensaver
ii cinnamon-session 3.2.0-20161111043005-xenial amd64 Cinnamon Session Manager - Minimal runtime
ii cinnamon-session-common 3.2.0-20161111043005-xenial all Cinnamon Session Manager - common files
ii cinnamon-settings-daemon 3.2.0-20161111004505-xenial amd64 daemon handling the Cinnamon session settings
ii cinnamon-settings-daemon-dev 3.2.0-20161111004505-xenial amd64 Headers for building applications communicating with cinnamon-settings-daemon
ii cinnamon-themes 2016.05.03 all Cinnamon themes
ii gir1.2-cinnamondesktop-3.0 3.2.0-20161111000245-xenial amd64 Introspection data for CinnamonDesktop
ii libcinnamon-control-center-dev 3.2.0-20161111013030-xenial amd64 utilities to configure the Cinnamon desktop
ii libcinnamon-control-center1:amd64 3.2.0-20161111013030-xenial amd64 utilities to configure the Cinnamon desktop
ii libcinnamon-desktop-dbg:amd64 3.2.0-20161111000245-xenial amd64 Cinnamon library for loading .desktop files - debug symbols
ii libcinnamon-desktop-dev 3.2.0-20161111000245-xenial amd64 Cinnamon library for loading .desktop files - development files
ii libcinnamon-desktop4:amd64 3.2.0-20161111000245-xenial amd64 Cinnamon library for loading .desktop files
ii libcinnamon-menu-3-0 3.2.0-20161111012008-xenial amd64 Cinnamon implementation of the freedesktop menu specification
ii libcinnamon-menu-3-dev 3.2.0-20161111012008-xenial amd64 Cinnamon implementation of the freedesktop menu specification
ii libcscreensaver0:amd64 3.2.0-20161111013004-xenial amd64 library and introspection data used only by cinnamon-screensaver
ii mint-artwork-cinnamon 5.2 all Default artwork for the Cinnamon edition of Linux Mint
ii mint-info-cinnamon 2016.01.11 amd64 Necessary information about the Linux Mint release and edition.
ii mint-user-guide-cinnamon 18 all The Linux Mint User Guide - Cinnamon Editio

Is "Effects on menus" a new option? I see fade effects on scrollboxes.
Ah, I think I see what the problem is. Turn "Window effects" on. This will show you the "Effects on menus" option. Turn it off, then try disabling window effects. Turning off the window effects setting should be disabling the effects on menu option as well and it may not be. If that's the case, it's a bug we need to fix.
Ahh, you're right! I've been copying my home folder for years and I guess I forgot that option exists. Thank you guys for the help.
I'm going to go ahead and reopen this. You did stumble on a bug on our side in the settings. We need to fix that so others don't stumble into the same issue.