The CPU supports AVX2, so this is weird; recompiling JTR from source (latest git with no option with ./configure) confirms AVX2 was used to build it as well, and calc_stat shows the following output with the same test:
zero -10log proba2[101256+115] (1) / 1, converted to 1 to prevent infinite length candidates
zero -10log proba2[115256+116] (1) / 1, converted to 1 to prevent infinite length candidates
zero -10log proba1[116] (1) / 1 converted to 1
zero -10log proba2[116*256+101] (1) / 1, converted to 1 to prevent infinite length candidates

Notes:

• Some tools don't really need such as calc_stat most likely don't need AVX2, so it may be worth compiling a part of John with AVX2 and take some of the binaries not needing AVX2 by compiling it with --disable-simd
• It may be possible other JTR tools are failing as well, only calc_stat was tested.