huzzah!
I was playing last night with a few ideas since its only on first run after an install that people seem to be able to reproduce it.
However, I have no distinction between first run after update and any other run.
The *only* time something different occurs is the first ever run - this is when it detects there is no ~/.liqbase folder and goes about constructing it.
I am at the point of thinking its something in the background occuring when first run happens, whether its the interaction between webbrowser->app.manager->liqbase or something along those lines.
After installing liqbase app manager does a refresh cycle and builds up its list, during this it pops one of those event notification thingies.
What if that is conflicting with the timing required to do first run.

I've attempted to completely overload my system by running everything possible (i had youtube playing and email configured and console windows open and app manager running and as many applets as i could running and the only time I managed anything different (beyond slowing down..) was when i was playing a movie which pre-allocates the xv window and prevents clean startup.

I've made a big note of it on liqbase.net and I'm gonna put it to the back of my mind for a while - like other things something will come to light eventually.

As for the (temporary) log, it is stored inside ~/.liqbase/liqbase.run.log
if you open the console and type something like
cp ~/.liqbase/liqbase.run.log ~/MyDocs/liqbase.copy.run.log

a copy of it should become visible within the file explorer.

I'm gonna stop it logging by default because the few that I have seen do not indicate any kind of issue and its so sparodic and unreproducable (it doesn't feel like a memory leak or sometihng because it can hit on very first welcome screen and remains until reopened)

Time to get back on with actual coding I think
If anyone has any more suggestions please add to the bug report on garage.