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If you select the THINK client's information page (the i icon on the main screen), you'll see the current molecule name at the top left of the largest section. The name has the following general format: 123-456-xxx, where xxx can either be blank (for the root molecule), or be a number between 1 and 100 (indicating the nth derivative of the molecule being processed).
Each work unit to be processed, that you receive, includes a set number (100/200) of core molecules. Each of the 100/200 core molecules has a name (123-456 in the case above). The client can form up to 100 derivative molecules from each of these 100/200 core molecules. Each molecule plus any of its 100 derivatives can have up to 1,000,000 conformers. The first derivative molecule (represented by the -xx) is -1, the second is -2, and the last is -100. When derivative -100 is processed, the processing for that molecule (123-456 in the case above) is completed, and a checkpoint may be written. Whether a checkpoint is written or not at the end of the processing of a given molecule or molecules is dependent upon how quickly the processing or that molecule or molecules has proceeded. On quickly processed work units (i.e. under one hour) I've seen the client not take a checkpoint for several molecules in a row. You can generally judge when a checkpoint has been taken by the sound of a little disk activity that occurs right around the processing of the -100 derivative.
Regarding de novo structures that you will sometimes see being processed when you're watching the graphical display. Sometimes a molecule may have extra potential if it's slightly altered in some way. The client attempts small variations or substitution of atoms to increase the number of molecules being evaluated. These newly altered molecules are the de novo derivatives, or structures, which are also processed by the client.
The completion percentage is non-linear (i.e. it does not represent wall clock time), but rather indicates the number of completed core molecules within the set of 100/200. This is because the client has no way to determine how complex a core molecule will be until it has been processed. Therefore when you note that the completion percentage has not changed for a while, first check that the time is being updated each second on the main screen and the legend says "Primary task is executing...". If you find these conditions, switch to the information screen to see if the derivative number, the conformer count, the de novo structure count, or the hit count, is increasing. It depends on how fast a machine you have and what else it is doing at the time as to how quickly these numbers will be changing.
If you need to stop and restart the client, try to do so as quickly as possible after the client has written a checkpoint (derivative -100 for the current molecule was processed) so that you'll duplicate as little processing time as possible when you restart the client. When it is restarted, it will not redraw the current molecule, but will wait until it begins processing the next one before updating the display. When this is the case, you'll see a message near the top of the information page that states "Structure not ready for display". This is a normal condition and the message is nothing to be alarmed at.