I've used both iMovie3 and iMovie4 (iMovie4 is much improved over 3) and had not had a single trouble importing clips, but I haven't done it quite the same as you. I've only used a miniDV camcorder and when importing from this, iMovie automatically detects the pauses and creates a new clip every time recording was stopped or paused. Since my camcorder does not have a pass-through feature, to convert analog to dv, I've had to record the analog onto tape first, and then import. Although it would be so nice to use on-the-fly conversion, my slow method has worked flawlessly. FWIW, I have a Canon Optura Pi (about 2 yrs old) and used it with the first generation TiPowerbook and the newer Al PB.
Go the slow route, it'll work. Since it's set and forget, do the conversion while you're making dinner or whatever.
Good luck.