In the end, chunks fail to load or register at a certain point. This was discovered about a week ago and has since been a continuing problem. The world was pre-generated using WorldBorder on spigot 1.8, and when a player is building out on the end, at random times the blocks that they're building with will turn invisible when they enter a chunk. These blocks are sometimes passable, and can be fallen through, but sometimes solid, invisible blocks. We also noticed an extremely critical issue, and that is random blocks (specifically dirt) being generated in a perfect pattern for whatever chunks have been generated. For any chunks where blocks are invisible (the broken chunks when a player builds out) that chunk also refuses to load any entities that a player drops.

SCREENSHOTS:
1. Here is the random structures in a perfect pattern:
http://gyazo.com/1a1e375915b171281af8863d00021870

2. Here is the invisible block that occurs when a player enters a chunk / area as their building out
http://gyazo.com/1f99102d4d292a03ad92b27230b95464

3. More evidence of invisible blocks, randomly occuring
http://gyazo.com/a9d124ccbc0b865aacff6b524b3a0a6e