I've seen most ethernet problems be resolved by doing a few things.
Use a cable that is sheilded and has a "Drain Wire". Wind blowing across the cabling on the tower will cause static electricity buildup and without drain wire it can damage the ethernet port. Note that the drain wire should only be grounded at one end.
In addtion to the drain wire - the gel filling prevents (though doesn't completely stop) moisture from flowing through the cable.
Do a google search for the following -
1000FT Cat5e Direct Burial & UV STP Shielded w/ Double Jacket Outdoor Bulk
If the problem is persistent you can try installing and ether surge device like this...
http://www.titanwirelessonline.com/PCB- ... isg-48.htm
I will say that the ether surge device can actually degrade the signal on the wire and make the link unstable over long runs...so be sure to throughly test it once you have it installed.
Finally, in addition to the POE runs that you have going to the base of the tower....you can run an additional line directly from one radio to the other for redundancy in case the first one dies. One way to configure the network redundancy is to create an EtherBridge on both radios that initially only includes the main port. If the main connection dies...you can Mac Telnet into the backup port from IP Neighbors (thank you Mikrotik!) remove the dead port from the bridge and add the backup port.
Hope that helps.