Some possible solutions.. some may work for ya, some may not.
1) Have something planned for "the other group". Part of the problem as you described it is that the other PC's are bored outta their minds. So give them something to do. Instead of "running away" the bad guys /blow a horn/ and run away.
Reinforcements come.
It does expand the combat- for sure- but now the party is effectively split but both "parts" have something to do.
2) Alternatively: If you expect your particular group to give chase with only a member or two and the end result is all but fortold.. Fortell it.
"after a few minutes of running you catch up to the goblin and kill it".
This saves the most time, especially if the guy was just running off to hide and hope the big bad PC's never came back.
3) Plan a "side trek" specifically to teach the PC's not to do this. it sounds like you have 2 PC's who like to split up and take off from the group. Bad, Bad PC. "Thou Shalt Not Split Up" should be engraved on their foreheads by now. If you have to give chase, give chase as a group.
It can be as easy as having "help" not be nearly as far away as the PC's think. (especially in an aquatic environment or while flying.. over the next rise isn't just another valley but a small village or war party.. )
4) Talk to the PC's about it. Some things are just irrelevant digressions to the story and as much as we hate to admit it sometimes Our Time is a very real factor. I know in the group I'm currently in, we play once a month if that. A 2 hour *absolutely pointless* diversion is a huge waste of our overall available time. While its totally metagamey sometimes just talking to the PC's can solve some of the problem. Be wary with this though as once you Do this /you can't have something run off/ and it be bad for the PC's.. because you asked them not to go giving chase. (or at least not to go chasing every single rabbit in the field dead).
Just some thoughts.
-S
The best solution to your problem, IMO, is stop trying to escape in the first place. It will save you a lot of time and energy if you stop having the npc's run away to begin with; if you know that your pc's are going to give chase and waste time, then you should stop.
Me, I almost always do my best to prevent escapes; I've grown tired of every schmuck npc who manages to evade our capture returning with 50 of his schmuck friends whenever we let our guards down. Quite frankly, it would be foolish not to give chase.
And as for the pc's being hindered while chasing our dear schmuck in the woods, just remember that the same applies to the runner. He may have time to run 120 feet away from the heroes, but let's remember that blindly running through the woods at top speed is dangerous. If he decides to yell at the top of his lungs in an effort to alert some of his schmuck allies, then he too is at risk of attracting random animals or monsters.
I really like the GMG rules for chases- but they are hard to do on the fly, and it's difficult to have generic ones prepared for all occasions...I hope Paizo makes some cards for it, I'd buy them.
But in reality, whenever this happens, I remind the players of the number one rule of adventuring: Don't split the party. In one campaign I kept using this one particularly evil ghost, who had free reign in the city they were in. He became their favorite (or most hated) foe, quite quickly.
Seriously though, it's really selfish of them to leave people behind, I don't feel bad for punishing them. It's a team-building exercise.