After going to a sector with a reddish look, my textbox turned red. Then when I went to the nav screen the lower part of it was also reddish. The size of this anomaly was about the size of the textbox on the station screen. When logging out this texture was still ontop of the options screen...

Hmm. Can you recall what sector that was? I'd like to check that out.

It sounds a bit like the problem might be that you had opened the chat console and used PageUp to read back into the log (which turns the console box red), and then didn't PageDown to the current text.

Yes, that's what it is. Scroll your chat box back down.

But uh, yeah, it probably shouldn't do that.