The number of clusters (ref 1) on a disk is one of the keys to determining the FAT type (ref 2). Typically, if it's less than 4096, it's FAT12; if it's greater than 65535, then it's FAT32. Otherwise it's FAT16.
Here are two ways to get the number of clusters on the disk (option 2 gives more detail if #1 doesn't reveal anything unusual)(ref. 3):
Use the Windows command prompt CHKDSK utility. Run "CHKDSK X:" where X: is the drive letter for your CF card. It'll tell you "the type of the file system is [FAT|NTFS]". The "total allocation units on disk" is the number of clusters.
Run a FAT/partition analysis utilty. One such shareware app can be found at http://www.runtime.org/diskexpl.htm (get the FAT version, not NTFS). The application will tell you if the disk is FAT12, FAT16 or another format. But to make sure there's not an odd formatting error, estimate the number of clusters on the disk by dividing "Sectors on drive" by "Sectors per cluster".