The connectors supply the same voltage, assuming they both have all four wires. Your PSU will determine the amperage, should they be on different sets of wires with different amperage supplied to different sets.
Some connectors will only use one pair of wires. (One pair is 12V, the other 5V.) If the connector you're having trouble with only has one pair of wires that would be the problem. If not...?
In the attached picture (ignore the SATA power connecter) you can see that the two sizes of Molex connectors are actually wired in parallel.