Often, motherboard trays allow you to place a lot of standoffs all over the motherboard, but you don't need them all. The problem is, is that it's quite easy to put some standoffs in the wrong location and not realise until later. These brass standoffs in the wrong location can cause a short.@darael, yeah i think i have missed it but i have checked all the standoffs and their position and they all seemed fine, if they can short the motherboard why are we advised to use them? And can you buy plastic ones because they wouldn't short the mobo should they?
As a rule, I count how many brass standoffs I put in the motherbaord tray, then count how many screws I put in. Then I check the screws are secure - this makes sure the screws are actually in a standoff.
The next time you get a motherboard, test it on plain cardboard first. Then you can rule out whether or not the installation into the case is causing the problem or not.