The rule text of Dispel Magic says for the targeted dispel:
Targeted Dispel: One object, creature, or spell is the target of the dispel magic spell. You make one dispel check (1d20 + your caster level) and compare that to the spell with highest caster level (DC = 11 + the spell's caster level). If successful, that spell ends. If not, compare the same result to the spell with the next highest caster level. Repeat this process until you have dispelled one spell affecting the target, or you have failed to dispel every spell.
and then it makes a practical example:
For example, a 7th-level caster casts dispel magic, targeting a creature affected by stoneskin (caster level 12th) and fly (caster level 6th). The caster level check results in a 19. This check is not high enough to end the stoneskin (which would have required a 23 or higher), but it is high enough to end the fly (which only required a 17). Had the dispel check resulted in a 23 or higher, the stoneskin would have been dispelled, leaving the fly intact. Had the dispel check been a 16 or less, no spells would have been affected.
This is what I find really confusing: why would the same target have effects which have different DC?
Do I need to compare to the actual caster level, or to the lowest level required to cast some spell?