It's been about a year since I've worked with HD, but it sounds to me like you have a bottleneck in disk-read or in your render. It's not a concern in that your exported video will be fine, but it's a hassle when you want to preview.
My 2cents is that it's the HD that's doing it-- it really taxes the system.
Since it's just those transitions causing the problem, I'd just render them and be done with it.
One thing I've done in similar situations is to cut the video before I add the transitition. That is, if I'm going to do a 10 frame dissolve, count in 10 frames, make a cut on that video on the timeline... then apply the dissolve only to that little bit of video. Otherwise, when you apply the dissolve, FCP thinks the whole big piece of video needs a render.
I hope that's helpful... again, I think it's the HD taxing your system, not anything you're doing...
PS. I've found this site to be very helpful:
http://creativecow.net/
Look in the Final Cut Pro area, under Apple
If you identify yourself as a newbie they'll trip over themselves to help, provided you've done some searching and made sure it's not been answered already