I haven't been in your situation where a postive turned negative after such a period of time, but the following web site indicates that different results can be obtained not just through a different test (ISA) but also whether whole blood or blood plasma is used. In fact, there seem to be a number of variables.

http://www.vin.com/mainpub/feline/aafpfelvdx.htm

My own experience was a litter of 3 kittens where one, by far the weakest, tested positive on the ELISA at 8 weeks but other two were negative. The positive kitten was isolated. Six weeks later all three were re-tested and that showed the original positive cat was still positive, one of the negative cats had become positive (Seshat) and the other (Ted) remained negative. Whether this was because the positive kitten infected one of the other kittens during the first eight weeks, we don't know. The two positive kittens were isolated together. The weakest kitten (Roo) died at 8 months. I continued to have the positive and negative kittens tested and they remained the same even though I reunited Ted and Seshat and they lived together for the next 6 years. Although Ted always tested negative, he definitely had a weak immune system.

I'm really pleased for you that one of the cats apparently threw off the virus.