I had the same problem because I went from a P&E Debugger Rev C. to REV D.
I addition to the request of the latest uint_cfz.dll version 3.59 made to P&E saw that the problem can be resolved only by putting in series with the CLK line of the BDM a 22ohm smd from my hardware project and everything is working again properly.
This was also recommended by the MCF52259EVB.
I hope I was clear and help.