Is it possible for you to switch to the 3.12 kernel in the TI SDK? I noticed that you are using a mainline kernel 3.15, this is not yet supported by TI.
With the 3.12 there is a documented problem with taking the interface up/down using the ifconfig command. The problem that you are seeing is different. One being that are able to recover the link. Also the sequence that causes that problem does not seem to apply here.
Is there just one ethernet interface on the AM3335x?