Discjuggler won't cache.

So on certain .cdi files I'll get a buffer underrun write error. The cache bar starts moving up until it get to about 39% then it drops off and errors.
Near as I can figure is my cd burner won't burn audio under 4 seconds. This can be a problem with those single "filler" files in the cdi.
Is anyone else having this problem?? Is there a fix?
Also, if I use cdirip what are the specific commands to use on dreamcast backups?
Is there any other way to extract .cdi?