The first thing I'd check is whether the user the scheduled task is being run as has access to the Moodledata folder (the location defined in $CFG->dataroot) which I think is what you're suggesting.
But if you've got two nodes presumably the Moodledata storage is being presented as some sort of mapped drive? So you need a user for your scheduled task which can access this location. You could try a test with a batch file containing something like:
DIR path\to\moodledata > logfile.txt 2>&1
Then configure a scheduled task to run this batch file as the same user as the existing cron task and seeing if it can see the files in the Moodledata folder.
If the IIS user is being used to run the scheduled task it could be that the IIS site user is different from the IIS user used for the scheduled task. In a single site/single node environment this user is usually the local IUSR account but this could vary (this is how I'd determine the user in a single node environment).