Hello,
I agree that your symptoms strongly indicate an issue with DDR3 communication or general system instability.
There are many settings inside of the preset.xml file that are very important for the ZYBO to operate correctly. I recommend that you start by using the vivado board files (thanks Dan) and run block automation on your processing system block after it has been inserted into the block diagram. This will make all of the important settings match what they need to for the ZYBO. Then you can make any application specific changes that you need.
The reason I am recommending this is because I see from your screenshots that you are specifying 33.333MHz as your input clock. The ZYBO has a 50MHz input clock (see PS_CLK on the schematic), so basically all internal PLLs are going to be generating clocks that are far from correct. This could result in highly unexpected behavior. There are other settings that are likely to cause you problems further down the road beyond the input clock, which is why I recommend just starting over and using the board files.
You mention we call out the ZYBO as supporting 533MHz. I apologize for this, as it is not correct. The ZYBO only works at 525MHz due to PLL restrictions when using a 50MHz input clock. If you point out where we made this mistake I will get it fixed.
