If you are just using a single external drive for all scratch disks then you are basically reading all the data from one drive, the computer is transcoding it and writing the new data back to the same drive you are reading from.
Its trying to get the drive to shift a lot of data around all at the one time, two seperate drives would be better, one for you to have your source data on -the H264s for the camera, this could be set up as the capture scratch disk (although this termonology is slightly outdated)- and a second hard disk for your computer to write the (much larger) transcoded files to, set up as the render scratch disk.
This would keep the data flowing through your machine, rather than putting all the data in one place and the disk struggling to read and write at the same time.
The shorter movs are playing back from RAM, which will be lovely and fast, but of a small capacity, the longer movs are being read off from the drive, which isn't fast enough.
64 bit processing is great, 64 bit OS is great, 64 bit apps are great, loads of RAM is brilliant, but the real speed killer is and always has and always will be the speed at which the data gets around your machine, the hard drives are the weakest link in the chain, and a fast interface is not the same thing as having a fast drive connected to that interface, and this appears to be the root of the problem.
I've not used a PC in years, but in terms of the hardware being more or less equal, RAIDs have vastly reduced my rendering times and vastly improved my playback quality and system stability. For fluid editing with massive data rates, such as the transcoded video files, you are going to need to look at either a couple of SSD's or internal / external RAID HDD's.
Sorry man, but thats the nuts and bolts of it.