Umberto:
I found a response in another forum on this exact problem (see below). I am going to turn off backcourse tonight and give it a try.
Bill
Your problem is the way Microsoft setup the default ILS in FS2004 and FSX.
Rwy 4R and 22R share a frequency (109.50), Rwy 4L and 22L share a frequency (110.90) and Rwy 13L and 31R share a frequency (111.50) at KJFK. And every one of those ILS is set to enable the backcourse.
Which means that if you are not exactly on ILS course, your aircraft will 'capture' the backcourse from the wrong runway. Of course there are not actual transmissions in FS - just a simlation of the effects of radio transmissions.
This in not a problem in the real world because none of those ILS transmits a back course, and the ILS for the runways not in use will be turned off to not transmit. But because Microsoft chose to Enable Back Course for every localizer in the entire world - several airports have this issue.
There are two options which should relieve your problems, but both require the airport to be edited.
1) Edit the airport to uncheck the default setting of Enable Backcourse on those six ILS at KFJK, or,
2) Change the frequencies of one of each pair of shared frequencies.
Nr 1 works most of the time for most folks. Nr 2 has the disadvantage of making it harder for you to find the new frequencies if you forget.
Something else is that you need to be able to recognize the identifier of the localizer your aircraft 'locks' onto. Some FS aircraft have a HSI gauge which will display that identifier, some will require you to listen to the morse code to recognize the ident.
Of course, you have to do your homework and know which is the correct ident, and what are the other idents for the airport should you 'lock' onto a wrong one.