I built my home a few blocks away from my starting point (spawn), so that I knew my compas would always guide me home, and for the week I've been playing it has. Until today. I got lost in some caves and had to pickaxe my way up rather than following my tunels back to base.

When I got to the surface, I encountered water and started swimming up. When I got over the blocks I'd dug out I saw something really weird. The light was almost like dusk and there was a bunch of strange creatures moving around even though I had peaceful on at the time. Then I started losing life and I realised I was still in the water and the creatures were Squids... Anyways, I was able to build a block over my head so I didn't drown. When I finaly got my head over the water I started following my compas back like many times before, only to realize it pointed to a snowy place that looked nothing like my home.
So, there I was - in a cold place and no map or compas that could lead me home so I took a chance and luckily enough I found my sky-tower and were able to get back home. Here I confirmed that the compas didn't point in the direction it used to (which would be on the lowest block on the tower). Anyways, I put my recently obtained diamonds and other minerals in chests and jumped off my tower to die just to check where I would spawn. I spawned next to my bed (obviously). When I went to check on my compas again it worked as it should; pointing towards my tower.

Again, I have not used any 3rd party programs, cheats or mods on this world. just plain survival mode. only thing coming close was that yesterday I tried out the server.exe file of yours on a world that I had downloaded.

To sum it up:
1. Water was nearly 100% transparent.
2. Compas got screwed up, but fixed itself when I died.