I think my personal peak acronym collison factor (ACF) for a TLA is 3. I once had to juggle three separate and valid meanings for "UPS": United Parcel Service, Uninterruptible Power Supply and Upson Hall (a computer RJE terminal at Cornell University). Now it's just two, like USB.
The building code for the Undergraduate Library at the University of Michigan is UGLI, which aptly described its architecture until a major makeover in 1993. Not Albert Kahn's best work.
Gillianren may remind us that to be a true acronym it must be pronounceable as a word, so the A in TLA may have to stand also for "abbreviation," giving us a metacollision of TLAs.
The LUT was originally going to be the
Saturn Launch Umbilical Tower.
The one that's most annoying to me is ASCI and ASCII. Both are pronounced "ass-key," but one refers to the American Supercomputer Initiative (those nice people who give me money to built ever-faster computers) and the other refers to the long-time standard for encoding text in digital form.