The most important factor in fluorescent DNA sequencing is the quality of the template . One common misconception is that if a template works in manual sequencing, it should work in automated sequencing. Automated sequencing is much more sensitive and often the quality of template used for manual sequencing is not good enough for fluorescent sequencing methods and will result in a little or no data. Many mini and maxi prep protocols produce DNA which is good enough for manual sequencing or PCR, but not for fluorescent sequencing. Also the use of phenol is not at all recommended as phenol can intercalate in the helix structure.
Straight chloroform is sufficient.
There are a number of DNA preparation methods which are recommended for fluorescent DNA sequencing. Promega's Magic mini prep or Wizard columns. The ABI recommended PEG precipitation protocol. When all other maxi and mini preps fail this PEG protocol usually comes to the rescue. It is very important to make sure that only one band is cut from the gel.