I installed my Windows 8 in a very similar way, and was left with many folders that required elevated permissions for write operations. Your .NET applications are probably under an account that cannot perform these actions, whether they be writing to these folders in general or elevating (I'm not terribly informed on how .NET applications work.)
Luckily the solution should be fairly simple. Take ownership of the folder.
For example my PerfLogs folder has some messy permissions (yes I realize PerfLogs has different permissions anyway, it was handy though). Try this with your logs folder. Open the properties and look at the security tab:
Click Advanced. You can see I don't have permission to even view the permissions. Your case might not be so extreme:
Click continue and take a look at the advanced security settings. Here's where I suspect might be going wrong for you:
If only administrators can write to your logs folder, and your .NET app isn't an administrator, logs aren't going to be written.
Dig around in to what user your .NET app is running under and figure out if write permission is allowed in the log folder. This won't be a hard and fast solution for you, because there problem isn't one. Worst case scenario, try adding
Full access temporarily to see if this solves your problem.