OK, a couple of things:
It's always a good idea to get RAM from the manufacturer's QVL list:
http://www.asrock.com/mb/AMD/FM2A88M%20Pro3+/?cat=Memory
It isn't absolutely necessary, as sometimes you can luck out, but it is guaranteed to work if you do. You also have the safety then if you call the manufacturer for customer support that they won't point to it and say "can't help you until you have approved memory in your system".
Beyond the QVL list, for higher performing machines (gaming), it advised to get RAM that is at least the same speed as the native memory controller. You're right, your board does support 1333Mhz memory, but your processor would like it to be much faster, with 1866+ being much preferred.
As for your current problem now; I can think of few solutions to explore. First would be, if you have the ability to RMA your two different sticks of RAM to get something that would work better, please do it. You will be much happier overall, and with something like 2133 or 2400Mhz kits, you'd be much more able to overclock, if you ever considered it. 1333Mhz just won't allow for it, and is possibly hindering your CPUs full turbo potential even now.
If not, then going down to 1 stick for testing and further trouble shooting is best. Because you were having issues with the first stick, adding a second unmatched stick would probably not make it better. RAM is always sold in matched kits because it was tested to work together properly, so when pairing unmatched sticks (even if the same make/model/etc, there is no guarantee from the manufacturer that it will work). Again like the silicon lottery in general, you can luck out and it will work, but sometimes it involves tweaking memory settings/timing/voltages to get it to work properly, or it just doesn't play nice in some or all situations (usually presenting itself under heavy loads, like gaming).
The last area to look at would be your UEFI/BIOS version. There have been system stability memory compatibility updates released since May, with the latest revision being Dec 22, 2015.....so while it isn't recommend to update your UEFI 'just because', when you're having issues, it's worth a try. When doing it though, use the memory stick 'instant flash' method......and never from within the operating system (this frequently causes problems, especially if you have system stability issues to begin with).