I sorted it out using an install disk of a previous version of OS
I would rather trust the later bug fixed version of HDToolbox. If it had not enough space then the earlier version probably didn't have enough space, too. It just did not detect it.
Now you are in danger that your first partition overwrites parts of the partition table and vice versa.
You should rather increase the blocks per cylinder value (and reduce the number of cylinders accordingly) so that you get more space in the first two cylinders which hold the partition table.
When using a CF card it's good to change the geometry anyway. This way you can align partitons to megabyte boundaries which is recommended for flash memory devices.
