Hello,
I am assuming that you took the Bakery specification from the Github examples [1]? However, the proof for the step that doesn't pass for you is in fact
<3>2. CASE /\ flag' = [flag EXCEPT ![self] = FALSE]
/\ unchecked' = [unchecked EXCEPT ![self] = Procs \ {self}]
/\ pc' = [pc EXCEPT ![self] = "w1"]
BY <3>2, Z3T(30) DEF Inv
Note the directive "Z3T(30)", which invokes the Z3 (SMT) back-end prover with a timeout of 30 seconds, indicating that the step may take longer than the default timeout of 5 seconds. This passes on my machine. If you have a really slow system, you may need to increase the timeout further.
In general, when a proof fails, it is a good idea to decompose it into smaller steps, such as proving each conjunct of the invariant separately, to understand which step causes problems.
Also note that there is a somewhat different version of the Bakery spec in the distribution of TLAPS, usually located in /usr/local/lib/tlaps/examples/Bakery.tla that should work out of the box.
Stephan