ProSites w/ PayPal Pro & Express - Dates Wrong/Ending Subs After Payment

Hello, our ProSites installation is acting very weird. Here's what's happening:

1. Recently all our settings reverted to default, resulting in 2 days of lost sales. We average $300 a day, so that's a big deal to us.
2. When a website subscription renews monthly, the next day the website (using Pay to Blog) turns off and declares that the website isn't paid for - meaning we have to manually extend the subscription by a month.

I can assist by providing any information that's needed, but if we provide access to our website through the dashboard then PLEASE DO NOT ALTER ANYTHING UNLESS YOU'RE CERTAIN ON THE OUTCOME.

Another note, our dashboard WPMUDEV plugin has to be deactivated and reactivated in order for it to appear on the menu.

* We can not deactivate all plugins, we've over 300 clients.
* We are on a dedicated server (managed) is this can help.

This is extremely urgent, as this is a critical part of our business we will either have to move to another system or have this handled.