Posting this in case it helps someone in the future. I still had this problem with version .67, although it was random and intermittent. I found a workaround by filtering by drive letter:
check_drivesize drive=all-drives "filter=drive in ('C:\', 'D:\', 'E:\', 'F:\', 'G:\')" warn=free<10% crit=free<4%
Edit: would you like me to update Bug #336, since it seems to be relevant to this issue?