This is why you shouldn't use modular PSUs. That melting has nothing to do with running a GPU off a molex, it has to do with a bad connection in the modular cable connection. If there was a good connection, the WIRE would melt, not the connector.
Most molex to PCI-E cables come with two molex plugs - use two different cables from the PSU so you're splitting the load. Less chance of melting the stupid connectors.