Hubby has similar problems. I couldn't tell you his statistics, but I do know that he looks almost anorexic when he trains hard.
Do you do any weight training at the moment? It doesn't have to be heavy stuff, but doing a session down the gym once a week, or something like Body Pump is a great way of building or maintaining muscle. You say that you can't put on muscle, but if you do something you will at least look toned rather than skinny.
The rest is just down to eating. Eat often and not just at meal times. Yes, you need your healthy balance to get your vitamins and minerals, but once you have your daily quota of healthy stuff then it is OK to fill up on anything else you want. Hubby nibbles on bread a lot, or handfulls of dried fruit and nuts, or even cheese. Take energy drinks before, during or after your runs and maybe have something like an energy bar or a cereal bar as soon as you finish your run. When Hubby starts getting excessively skinny I make muffins for him. Portable food is great because you can eat it anywhere and just grab and go. Hubby often has a muffin in the car when I'm driving him to work.
I hope you can take some ideas away from this.