First of all, I would transcode to ProRes (not necessarily ProRes HQ). The native format slows down your system a lot and is a very compressed format – specially for composite and greenscreeen work not very handy.
Slowing down your system? What is your system if I may ask.
Of course the HD Files are a lot higher resolution and therefore needing more horse power.
What system you use?
What version of FCP?
Do you transcode them with Log & Batch to ProRes?
What are the native files in? What you shot on?
Sascha