Thank you for your inquiry and the opportunity for me to do some interesting research.
From what I have found, Germany sent 62 U-boats to the Mediterranean from the beginning of World War II through May 1944. Interestingly, none of the boats ever succeeded in leaving the Mediterranean, all being sunk in battle or by mine, destroyed by air attack while at their base in Toulon, France, or voluntarily scuttled by their crews. That is not to say, however, that there were no successful U-boat operations after September 12, 1943. I have found records of at least 26 Allied ships that were sunk, damaged or declared total losses (i.e., not sunk but damaged beyond repair) from U-boat attacks in the Mediterranean after September 12, 1943, and as late as May 19, 1944. None of the Allied vessels lost or damaged in the Mediterranean, however, include SS WILLIAM B. TRAVIS. See http://www.uboat.net/ops/mediterranean.htm, http://www.uboat.net/ops/med-1944.htm, and http://www.uboat.net/ops/med-ove.htm.
As you have found, various sources disagree on what happened to WILLIAM B. TRAVIS. The Armed Guard website (using as its source “Liberty Ships,” by John Gorley Bunker, 1972), claims a torpedo attack; see http://www.armed-guard.com/ag81.html and http://www.armed-guard.com/ag68.html. A page from the website American Merchant Marine at War, http://www.usmm.org/medit.html, listing ships sunk or damaged in World War II in the Mediterranean, also suggests a torpedo attack. (Sources for this information are listed at the bottom of http://usmm.org/shipsunkdamaged.html.) This page, http://www.shipbuildinghistory.com/history/shipyards/4emergencylarge/wwtwo/toddhouston.htm, identifies damage from a mine (scroll to hull number 27). And this page, http://www.convoyweb.org.uk/ports/index.html?search.php?vessel=WILLIAM%20B%20TRAVIS~armain, showing the wartime operations of the ship, is silent on what happened to her in September 1943, although there is a gap in her operation between September 1943 and October 1944, with the implication that she was in Bizerta, Tunisia, that entire time. I know of no independent source to settle the question definitively but especially given the absence of confirming information at www.uboat.net of a U-boat attack on the ship, it is difficult to dispute the probability that the damage to the ship was due to a mine rather than a torpedo.
That said, there are a number of reasons why a U-boat commander might not pursue a damaged ship to assure that it sank. For example, in no particular order: the U-boat had expended all of its torpedoes; the U-boat was damaged by defensive fire from its target; the commander believed the ship would eventually sink due to the damage inflicted; the U-boat came under attack by warship escorts or by aircraft and could not continue the attack; other targets presented themselves; weather or sea conditions precluded a pursuit of a damaged ship; although damaged a ship might be able to maintain enough speed to outrun a U-boat if the U-boat was out of position to pursue or was otherwise preoccupied; the U-boat commander deemed too dangerous the pursuit of a damaged ship while in close proximity to land or to an enemy port. There could be other reasons. The list referenced above of Allied merchant ships sunk, damaged or total losses in the Mediterranean shows a substantial number of ships that were only damaged rather than sunk from a U-boat attack, so apparently it was not unknown for a damaged ship to escape further attack for whatever reason; see http://www.uboat.net/ops/med-ove.htm.
While I cannot offer a certain answer to your questions, I hope the above is useful.
Ron Carlson, Webmaster
Armed Guard / Merchant Marine website