I'm not really a brass player, though I used to be a band director and have some idea about brass acoustics.
The issue with multiple-valve combinations being too sharp is that the valve system is a compromise. Pretend for a moment that you have a straight trumpet with no valves (so, pretty much a bugle). Of course, you can play pitches in the harmonic series with it. If you want to lower the fundamental pitch by an octave, you need to double the length of the instrument. If you want to lower the fundamental pitch another octave, you need to double the length again.
With that in mind, say the trumpet is one foot long. If you add another foot, you lower the fundamental pitch one octave. To lower the fundamental pitch another octave, though, you now have to add two feet, not one. So, the lower you go in pitch, the greater the length of tube required to make the same interval happen.
Now, go back to the valved trumpet. If you push down the second valve, you lower the fundamental pitch a half step (approximately, but I'm getting to that). If you push down the first valve (alone), you lower the fundamental pitch a whole step. If you hold down the first valve and push down the second, you extend the tube the same length you did when pushing down the second valve from "open" position -- but the actual "ideal" amount the tube's length should increase is farther from the second to third semitone below the fundamental than it would be for the first semitone below the fundamental. Therefore, with no adjustments of any kind, the combination of valves one and two would be sharp. The problem is compounded when you go even lower.
Now, I said "without adjustments." I don't have a reference source for this offhand, but on a standard three-piston-valve trumpet, I believe the first and second valves are designed to be five cents flat, while the third valve is designed to be twenty-three cents flat. This design partially compensates for the effect I have described without making the notes that use fewer valves too flat to be usable. This is the compromise of which I wrote at the beginning of this answer. If you play (without adjusting your embouchure) a note with the first and second valves down, then play the "same" note with just the third valve, you will notice that the note with just the third valve is lower than the note with the first two. The fourth valve on a four-valve instrument works similarly to replace valves one and three, though I do not know the number of cents offhand.
So, combinations of valves two and three are reasonably in tune, but one and three is not sufficiently lower than two and three to make the semitone descent. Therefore, one and three is a sharp combination, which is why you pull out the third-valve tuning slide. Pushing down all valves is even worse, so you may need to pull out the first slide as well (or not, depending if you need to).
Complicating the matter further is that the curvature of the trumpet takes the harmonic series out of tune a little bit. On certain trumpets, this effect is greater than others, but notably, the fifth harmonic (written E, generally) can be quite flat. Sometimes, then, using one-and-two is recommended so that you are basing the pitch off the sixth harmonic (G) instead.
One last thought: if you want a visual of the increase in distance as notes descend, find a trombonist. The seven "traditional" positions correspond to the combinations of three valves that you are used to, but positions six and seven are much farther apart than positions one and two. Or, go look at a guitar's fretboard, since it's the same idea I am describing: each fret is a semitone, and the frets are farther apart where the effective string length is greater.