First, I want to stress two things: 1. Grounding your equipment properly usually solves wierd ethernet issues, I cannot stress the importance of good grounding on your equipment and the grounding of the tower you are using. In our case, we only use the Superior Essex copper clad cable and each run is grounded to the tower ground with a very thick and short as possible ground cable. Use thick ground cable not the cheap green stuff. 2. Ferrites help and I have personally seen them solve ethernet negotiation issues in high RF environments but are by no means a substitute for good grounding.
Due to our use of the copper clad cable, which is much thicker than toughcable or any other shielded cable I've ever seen, we are forced to use the snap-on ferrite cores. I get them online from Newark Element 14. I choose them for their specific diameter, ferrite material, and frequency range. You'll notice when you look through the the listing of ferrites that they have different oHm and frequency ranges. In my case, I knew FM was the issue and I suspected that the FM frequencies on the tower we were collocated on were the issue, I selected a ferrite that was in that range of frequencies and the most OHM's .
The more loops you run through a ferrite, the more OHM's of resistance it creates. Because you cannot loop these copper clad cables due to thickness, I simply stacked on 12 ferrites on top of each other at each end of the cable. Also important to understand about ferrites is that they do not affect what is going on "inside" the cable. Ferrites only remove or attenuate, or choke, the frequency being induced on the cable from the FM and turn that energy into very small BTU's of heat. What I mean by that is your cables on, say a 500ft tower you are on, are being blasted by all kinds of RF energy from AM to FM to your own equipment and that energy flows along the cables and literally makes the cables an antenna for that AM, FM, or whatever. That energy, if left untouched, WILL enter your radios and network equipment and cause you tons of hell. Some people say to move the CMM up the tower to shorten the cable runs and this works sometimes as well because you are essentially lessening the noise entering your equipment. The HAM guys will tell you that they put chokes on their coax because FM will get induced and it will produce a spark when they talk into the microphone. We once put a toner on a cable running up the tower to locate the cable and could listen to the FM radio station through the toner that was touching the cable!
A couple different ones I've used:
http://www.newark.com/webapp/wcs/stores/servlet/ProductDisplay?catalogId=15003&langId=-1&urlRequestType=Base&partNumber=81C7667&storeId=10194
http://www.newark.com/webapp/wcs/stores/servlet/ProductDisplay?catalogId=15003&langId=-1&urlRequestType=Base&partNumber=72K6749&storeId=10194
It is important to understand that the reason these things fix ethernet negotiation issues is because they remove the common mode RF noise that is being induced by the RF environment. Because FM transmits around 100Mhz, this creates a huge problem for ethernet and you will notice things may run totally fine when the weather is good but during a heavy rain you will start having CRC errors and dropping packets like crazy. I've heard that in the Southwest USA, the dry dirty winds will cause static electicity and cause this behavior as well.