I had a similar problem. I totally confused myself by successfully running the wine version, then (magically, I at first thought) the native version started to work.
It looks like the problem is that scribe switches to the root user (uid = 0) and makes files under your HOME directory owned as root. Then you run it as yourself and it can't get at them, so it crashes (failing to send the error message in the meantime as it had all locked up).
The fix was to change the ownership of all files under $HOME/.nch using sudo (or su if you don't use sudo) and, for good measure, make them group writable. Put your username:group in the chown command (mine comes out as david:david; ubuntu gives you a group named after your user by default). If you aren't sure, type ls -l at a bash prompt (eg in konsole or xterm): the user and group are the first bits after the read-write-execute bits. (Sorry if I'm teaching granny to suck eggs here; not sure how far with linux you've got).
sudo chown -R username:group $HOME/.nch
chmod -R og+rw $HOME/.nch
While the linux native version is working tolerably well for me (I'm not a professional, I'm just doing some transcriptions for my wife) it looks as though there are some rough edges and some poorly-thought out issues to do with use of root.
I also treated myself to one of the recommended footpedals which skips 5 seconds FORWARDS when it restarts, which is less than helpful. That, I expect, is another issue.
EDIT: riddle me this, it isn't the footpedal, it's the (also new) spectra USB headset. If I use the default sound device (an old SBLive!), the 5 seconds skip goes away; if I use the Spectra headset, the ES counter skips ahead each time I take my foot off the pedal to stop playback.