As for runnign the game is it better to run each instance from its own folder or to run all instances form a single folder? I don't recall being able to actually pick the folder in which to run the wow.exe when setting up isboxer is this possible or is it better to just run all instances form one folder?
The only benefit you get from multiple folders is having multiple configurations.

Performance-wise and cost-wise you are better off having a single folder, and with ISBoxer virtual files you get the multiple configurations while maintaining the single folder benefits.

Without virtual files, people generally use symlinks to regain most of the performance of a single folder. However, there is still extra work to do on patch day to make sure all of your WoW folders are patched even if using symlinks. (Also not a problem with virtual files)

This sort of corruption is typically caused by... WoW crashing at just the "right" time, normal wear on your hard drive, or even bad drivers used by your hard drive. When SATA drives were the new thing, I remember having lots of driver issues with the drivers that were default in windows as well as shipped with the motherboards. Then now with the new SSDs, particularly of the Intel variety (or maybe only on Intel motherboards, I don't recall right off hand but google would probably turn it up), there's also a data corruption bug. There's probably other scenarios but these are probably the most common.

To be on the safe side, I would recommend checking for drivers for whatever sort of drive it is your data is on. Other than that, running the repair tool should have solved the immediate problem, so you're probably in good shape for now