The bug where animation names with numbers in addition to the frame index are mishandled was fixed in commit 454f714, but it now occurs again. Example name attributes of SubTextures in an affected TextureAtlas:
Anim10001
Anim10002
...
Anim20001
Anim20002
...
I believe that the earliest versions would combine all of these frames, then the behavior was changed so that Anim1 and Anim2 would be processed separately, and now I believe only SubTextures prefixed with Anim1 would be included.