You wanna field this one?
Probably not relevant to your problem but how is your RAID configured?
Block size?
Striped?
Where is FCP's scratch disk? On your eSATA RAID or your internal drives? Separate volume or same volume as your source files? Separate RAID disk or same RAID disk?
I'm asking more out of curiosity than out of the expectation that any answers you provide may provide the necessary clue to fix your problem. But if what I'm getting at is potentially the problem, hook up an external firewire disk and select it as your FCP scratch disk. If the problem disappears, then we'll have another clue. If not, then I guess you'll still have a problem and my curiosity will be satisfied.
Good luck! And I hope someone here can help you.
Having had the same problem using Final Cut Express, in researching possible reasons, I found that the reasons can be numerous and sometimes unrelated. I second the recommendation to check the FCP discussion boards at apple.com. That's the first place I go when I have problems.
I'm not an expert by a long shot, but I'd make sure all apps. are closed and internet connection cut off (even auto Software Update) while working with FCP. You need a lot of free space on your hard disk (15-20 gig is what I recall). Unless you have a monster hard disk, a firewire scratch disk is a necessity - but you probably already know that. Other basic things like recording in 16 bit, I'm sure you know as well.
If all else fails, sometimes software or software preferences just get corrupted. Sometimes trashing the preferences helps, sometimes you just have to trash the application and reinstall (speaking from experience).
Good luck in finding the problem. I've been there and can sympathize with how frustrating it can be.
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...
If you're only getting the problem with rendered transitions, your first troubleshooting item should be your scratch disk. If it's the same as your startup, especially with a sub 1-Gig system, you're going to have problems. Switch it to a drive that is, preferably, neither your startup nor your source.
If you're still having the problem this evening, I'll go through my settings when I can get to my system and see what else might help you.
This is your most important lead.