Yes, I feed him 3 times a day (I know they say 4 times at 12 weeks but he doesn't have a huge appetite!). He is like clockwork for his 7.30am poo and I suppose the same for the one he does in his cage at school run time (3.00pm). It's just getting him out of toiletting in his cage when I'm not there. I always spend 15-20 mins with him playing outside before I have to leave him in his cage alone but he won't do a poo then, will save it for when I have to go out. I have also put him in his cage beforehand and 'pretend' to leave, he does a poo so I can clean it up before I actually have to leave! It might work but I really want to stop it completely. I have kept a toilet diary since bringing him home to try to help me predict (sad, I know).
It sounds like you have the toileting sorted (i.e. taking him out before you leave for exercise etc to see if he'll go). Wonder whether, as someone else has said, it would be worth exploring the separation anxiety route. Don't know enough about it but maybe there might be a book on the subject. I hope something works out for you.