spectrogram cutting off at the end

Ok, I see it now.  Use Audacity and add a second of silence at the very end of the song.  That way when the spectrogram stops at the new end you'll be able to see the markings that were once "smeared" and can place events easier.

yes it was newly ripped and then used

just so you know.. when I switched over to amplitude it looked fine.. better than nothing and guessing

The spectrogram will be as long as the file is.  Therefore if you are seeing a weird "smear" at the end, then your first step is to check on the wave file itself using another program (just not the one you used to make it). 

If the file looks ok and it plays fine on another program such as windows media player, you could go to the cache folder in Aurora and delete any wav files.  Aurora will automatically extract the file again the next time the sequence is opened. 

Failing that, if this started off as a shared sequence, try using a longer file to see if there is an issue with the sequence itself, then revert back to the original file once you have eliminated any phantom commands. 

is your song a wav or mp3? Mp3's tend to make the sequence make funny sounds in the spectrometer