Please also note that this wasn't a missing corrupted chunk but appeared at my spawn location - around my mine and buildings.
I don't believe it is an operating system issue but a glitch with the program. I copied the file across to a back-up server and re-ran and the file worked. Based on the ticket MC-2545 it appears to have been causing quite a few end users / customer issues since release 1.4.4 and states fixed in 1.8.1 which is the version I am currently using with windows 8.1 (not in compatibility mode as per ticket MC-2545). Does ticket MC-2545 need to be re-opened?
Can I expect more of these gigantic holes to appear on my map?
Agreed - still an issue in 1.8.1 - see MC-75375. This issue should be re-opened as it certainly is not resolved