29.97fps is the actual frame rate for NTSC (North American) video. It has historically been called "30fps" for convenience sake. However in recent years true 30fps capability has appeared even in some consumer camcorders. This can result in some subtle problems if you mix real 30fps material in a standard 29.97fps sequence. The "change" you refer to could occur if your clips were recorded at a real 30fps and you put them in a 29.97fps sequence. FCE will try to conform the clips to the sequence settings.
For completeness, here is what FCE supports:
SD video at the following frame rates. FCE imports DV video as QuickTime/Apple DV during capture from your camcorder
- DV-NTSC @ 29.97 fps
- DV-PAL @ 25 fps
HD video at the following frame rates. FCE transcodes all HD video (HDV and AVCHD) to QuickTime/Apple Intermediate Codec during capture from your camcorder.