It looks like WhatsApp has begun to crack down on users of third-party clients for the messaging service today. The company recently began instituting 24-hour bans for users of WhatsApp Plus, specifically. However, there have been various reports of WhatsAppMD users being affected as well.
WhatsApp has officially acknowledged the bans via a support FAQ on its website. It states
WhatsApp Plus is an application that was not developed by WhatsApp, nor is it authorized by WhatsApp. The developers of WhatsApp Plus have no relationship to WhatsApp, and we do not support WhatsApp Plus. Please be aware that WhatsApp Plus contains source code which WhatsApp cannot guarantee as safe and that your private information is potentially being passed to 3rd parties without your knowledge or authorization.
WhatsApp then goes on to state that uninstalling the unauthorized application and installing the official app should remedy the situation.
As frustrating as this may be for users of these third-party apps, it really shouldn't come as a big surprise. Not only are the apps not listed on Google Play in any capacity (requiring side-loading the APKs to get them on a device), but they also make use of WhatsApp's network without permission. Really, it was only a matter of time before action was taken.
Thanks to everyone who sent in tips on this one!