Using BoxCryptor 1.7.409.131, there appears to be an interesting bug.
If you use the PowerShell Add-Content command to add information to a text file, it will miss information without any warning.
Try this on a BoxCryptor drive:
[int]$counter = 0;
while($counter -lt 1000)
Add-Content -LiteralPath "Test.txt" $counter.ToString();
If you run it through the Powershell ISE, you get better results but both fail fairly dramatically!