don't know where to start with all the information given
With all the information given tho, we still need to know log files, what sabayon you are using, what you last did/updated, you know the relevant things!!
Noting to tell, I installed Sabayon 3.5 straight out of the box. I tried to emerge octave but found nothing. I looked for gnuplot but I found nothing. All the standard scientific programs on sabayon which I would normally use aren't there.
As I just installed sabayon ,there would be no logs to examine.