The most obvious answer would be that you are doing something wrong. There are several studies showing that Farage cells can express EBV, so I think we can assume that the cells should give a positive signal.

I would suggest you review available literature and verify how others performed ISH on Farage cells. Check your probe(s), maybe try probes that others have shown to work. Include controls to verify that your ISH protocol works properly.

Well the protocol is actually the one that is used in diagnostics so it's reliable. The RNA controle probe shows that the RNA quality is fine and in the same run, I could detect EBER in another cell line. 

The most common thing that happens is that cell lines get cross-contaminated or miss-labelled and you end up having something in culture that actually isn't Farage. When was the last time that your lines were STR typed for identity? The easiest thing to do may be to go back to a very early freezing of the cell line (maybe prior to mix up) and see if you have success with that.

Since all your controls seem to be ok, I agree with Michael that there must be something wrong with your cells. Either find a very early sample or get some cells from another lab where they do test positive.

Good luck.