A factory reset using the "hdd recovery partition" or recovery CDs will restore all 3 partitions, since all 3 of those partitions were there from the factory.
A clean install of Windows will remove all partitions and create 2 new partitions: C for Windows and System Reserved.
Your problem may be a Windows problem because of something you did after getting the PC. Or you could have a hardware problem of some kind.
If you do a clean install, you will no longer be able to do a factory reset UNLESS you contact Toshiba and buy recovery CDs from them.
You may be able to make recovery CDs now from your recovery partition. The recovery partition and the recovery CDs have the same purpose. You don't need both of them.