Tradesman1 :
Might be DRAM... (it's not 'confused' as mentioned above and it's not likely to damage anything, other than the system crashing which could corrupt some files...
I would have to agree with Tradesman1, the different memory is likely not an issue. Modern MBs will set each stick of RAM at the same timing, whichever is slowest. If the PNY is slower with higher latency then the Vengeance will match the slower speed of the PNY ram. No harm done to the faster ram, you're just not getting that memory stick's full potential.
I suspect the issue may be your 120 GB SSD if you use that as your gaming drive and boot drive. You may be running into file write saturation where the small capacity SSD has to "take a breath" to clean up (garbage collection) some of the blocks on the SSD. Using a computer is a two way street, there are constantly writes and reads. Though with gaming the reads are much heavier than writes.
If you are using the HDD as your game drive, then you can ignore the last paragraph as it would not pertain to your situation. If that's the case, I would check the event viewer for any errors. To the layman, the event viewer won't make much sense, but Google is your friend.
Another issue could be heat related throttling or freezing. The R9 290x is known to run extremely hot, upwards of 90C. In fact both your CPU and GPU pump out a LOT of heat, so I hope you have adequate air flow. If you can, monitor the temps while gaming and record to a log. The next time your PC freezes check the log. Usually the GPU is throttled when it overheats, but it has been known to cause freezing and stuttering amongst other issues. Not to mention if the heat is saturating your case interior, it can cause your CPU to throttle or freeze or your SSD to freeze. Heat is your #1 enemy.
Final note: it's hard to diagnose an intermittent issue especially without being hands on. I have several years IT experience and intermittent issues that cannot be reliably replicated are very hard to diagnose.