Where do i find details of short cruises (3-5 nights) starting and ending at San Juan in October 2008?

There are none that I'm aware of. They are all seven day.

There was only one and was with RCCL on

"the empress of the seas"

You visit st.Thomas and St. Martin.

I was looking the other day to take a short cruise this next christmas, but as later I found that the only one posted on their site is a short cruise in the Adventure of the seas but they don't let you book it for some reason, I suppose they cancel it and it's still on the server don't really know why,

If you are looking for a short cruise but not ending on San Juan, Carnival Victory has an option where you can disembark on other island three days after embarking on San Juan, My advice:
Check carnival.com or royalcaribbean.com they are the only two cruise companies that I can remember, that do short ccruise from San Juan