Hi, Pawel-

What version of linux do you have? That is, what is the output of:

lsb_release -a

Note that you can preserve your tailorings (though, I'm not sure by what you mean as your "smoothing" in the AFNI GUI?) by setting values in teh ~/.afnirc file. As part of the installation instructions, these can be initially created during installation as described here:
[afni.nimh.nih.gov]
.. and then you can edit it further; the descriptor help for AFNI environment variables is here:
[afni.nimh.nih.gov]

I don't know what a power outage would have done/changed. For starters, what is your PATH on the machine:

echo $PATH

And what is your display:

echo $DISPLAY

Note that you have click on the VcXsrv Windows X Server icon *each time* before starting your Linux terminal-- that is just how Windows designed things for allowing X-stuff through the terminal.

--pt