I've had these problems numerous times now and I'd love to get to the bottom of them as it's affecting the business of our site.
The entire Pro Sites network settings have just vanished again, except the account levels and upload quotas, as if they've corrupted themselves and reset to default. All plugins and themes that I'd set up, PayPal details and prices are gone and it takes me over an hour each time this happens to re-set everything up again. Disabling all plugins to find the culprit is not an option as we have thousands of customers, I can see no reason why anything we would have installed would mess with the settings. I'll list everything we currently use:
* All these plugins are network activated, we also use Multi-DB.
Server set up is Ubuntu 10.04 LTE, nginx, php-fpm with APC, MySQL, no object-cache, no WordPress security plugins or plugins that change core features randomly and WordPress 3.4.2.
I'd previously been restoring the psts_settings table in the wp_sitemeta database, but this time I don't have a recent back up. It hasn't actually done this for a while now, nothing has changed since last night to make this happen.
Also, I had a customer the other day who had had their Pro account status withdrawn automatically, and then sent a receipt and charged again by PayPal, even though they had 6 months left on their account. I tried to refund the PayPal payment via the plugin but it just said that it had found an error, that was all. Account statuses are withdrawn from people regularly at random by the plugin, or culprit of the problem, but this was the first time I've seen it charge again. This, to me, is quite worrying.
Do with that what you will, I'm more than happy to work with anyone that will help rectify this. It is a major problem and needs fixing immediately, although I know no one else seems to have the same problem as me, or at least hasn't noticed it yet.