I have no clue why this is happening - it makes no sense to me. Hopefully it does to someone else here...
We have a large (underground) rain water tank. This connected to the house's water system and allows us to have rain water coming out of the (cold water) tap in our utility room and to flush each of our toilets (one on the ground floor and two on the first floor (en suite and main bathroom)). It uses a pump to do this.
If we choose to, we can close off this system using two taps (I know that's not the right word) on the pipes in the garage and utility room and instead feed off the mains.
This morning my wife switched to the mains supply because we have family staying with us and the pump for the rain water system is quite loud.
Here's the bizzare bit...
Last night, all three toilets were working normally. After switching to the mains supply the toilet on the ground floor and the toilet in the en suite worked normally. However, the cistern of the toilet in the main bathroom did not fill up (the shower, bath taps and sink taps are drawing water as normal).
My immediate thought was that (coincidentally) the toilet had developed a fault. However, after switching back to the rain water system it is working again.