I've recently been having the same problem. Everything will work fine for the first ten minutes or so, then things start getting wonkey. The RF output fluctuates as does the SWR.  I've basically had to turn everything off and then switch it all back on and that has seemed to fix the problem at leaset until the next time.  I haven't changed any settings, I haven't done anything with the antenna cables, I haven't done anything with the power cord. All these problems just seemed to start happening out of the blue.