As Kev says, more likely to be the Doughnut.... mmmm! Doughnuts!!! errr, Anyway...
If the bolts do come through the base of the cistern then they could well be leaking. More info needed matey. But assuming they do, did you use rubber washers? If so, what size? You need decent sized ones and nice and thick too. Bl**dy suppiers should supply decent ones but seldom do!
Its pretty obvious to any DIYer that the stud comes from somewhere!
The top of the stud is a bolt INSIDE the cistern. This has a flat metal washer and a thick rubber washer on the inside and a plain nut and a metal washer on the outside ( usually ).
The threads extend downwards by about 50 mm to form the studs on which the wing nuts are screwed to squash the doughnut and hold the cistern onto the pan.
Need to edit to add that there are also some, usually older ones, where the stud does not go into the cistern and just starts at the top of the metal plate. In that case if the donought is properly squashed and the cistern correctly located then there is no scope for it to leak.
There were some thick flat foam plastic/rubber washers to do the job of a doughnut. They never sealed properly and should be replaced with the correct doughnot type.
Take the cistern off the pan and check the dohnut washer is seated correctly, if it is and still leaking buy another one. These also sometimes leak if the gap behind the cistern is a bit wide and is forcibly screwed back to the wall.
It's annoyingly common to find that if you put the cistern on the pan and do it all up, the cistern leans forwards by 3cm. If you create a wedge shaped donut to tilt it back it will seal but you see a gap at the front between p & c.
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