That's strange, I'd think the external to be much slower. You should definitely try and rule that out as causal.
Check what speed your drive is operating at, if it's in PIO mode something is wrong with the driver or how the OS sees the drive itself, possibly registering it's capabilities incorrectly.
If it's showing "DMA" or "UDMA" then it's registering itself correctly and should be operating at normal speeds. You can find this by dicking around somewhere in device manager.
You can also test read/write speeds and the settings with something like
HD Tune.