It is not uncommon for water to remain in the cistern it can depend on type of syphon and flush mechanism you have. Some flushes give a half or a full flush depending on how they are operated. Some syphons are adjustable to how much water they let out in a single flush. eg if your flush is set to say 10lt and your tank holds 12lt then 2lt will remain etc. It may be that the level is a little too high meaning water is not all used. Most cisterns will have a fill level marked somewhere on the inside. Try adjusting your filler to this level.
However I would say that as long as the flush is good enough to clear the bowl then dont worry.
Robin S
September 2008