After locating various similar ware + rep situations as those that caused trouble in X3TC I was unable to observe the Mk3 stall on a rep-disallowed ware or other rep related stall. Tested as noob and low level ST, beginner UT and level 25 UT.
There are other quirks but nothing that simply stalled the Mk3 from working.
IE: I have had to break the meatsteak cahoona loop a few times. I've witnessed up to 4 sequential trade runs by a level 25 UT, of buying 3 meatsteaks to sell at the trade station in Treasure Chest. Basically the UT pops into Treasure Chest and becomes a ST for as long as the IS cahoona loop lasts.
Sure won't be buying averice with that sort of pilot dedication.

Just for FYI to any X3R players reading this. I have found eventually the Mk3 will go into standby, waiting for the market, in Empire's Edge. While this is a good sector to be sure, I have -never- seen a ST go into standby in Patriarch's Retreat. Perhaps due to the size of the sector. Nonetheless I am inclined to think Patriarch's Retreat may surpass Empire's Edge in both earnings and pilot training.