Alan,

The fight for the Judah was a pretty intense affair. The Union boat party attacked the vessel at about 3:30 in the morning and later reported a fierce fight with C.S. Marines and sailors. The ship was finally seized after the Confederates were driven onto the adjacent wharf. There they were joined by a detachment of guards and a steady fire was maintained on the Federals until the mission was completed.

General Bragg subsequently attributed the loss of the vessel to the desertion shortly before the attack of several Confederate Marines who fled to the Union forces in a small boat. He also claimed that there might have been some neglect on the part of the guards aboard the Judah, but Union navy officers indicated otherwise.

Here's a link to Ed Bearrs account of activity at Pensacola Bay at the time. He devotes a couple of pages to the Judah incident:

http://fulltext.fcla.edu/DLData/SN/SN00154113/0036_002/36no2.pdf