A couple thoughts.

The first may sound obvious, but: cell times are based on 29.97 frames/sec. regardless of if the film is progressive or not.

If you've found the chapter locations yourself using just about anything (VirtualDub, etc.), your numbers are probably based on 23.976. Multiplying by 1.25 will fix that.

Also, if your cells are ripped using DVD Decrypter, they may also be wrong. The program doesn't handle NTSC cell times well (only PAL). Grab PGCDemux and try reripping just the celltimes.