I would suggest installing the old version of X-CTU. The new and the old versions can be installed and used side-by-side.
X-CTU version 184.108.40.206
If your module doesn't work currently, I would try the Recovery Method found at the link below:
XBee Recovery Guide
As for the error you show, I will try and replicate what you have seen. If I can replicate it, I will report this to Digi software engineers.
You might also try loading a previous version of the firmware (10E6). This would verify that it is file specific and not a problem with X-CTU NG.