I just tried to replicate it and it appeared in the shop for me. idk if you are going to play another round, if you do, can you try to not pick any star upgrades and see if that fixes the problem?
After some testing, it seems like if I start a new run but close the window before unlocking the scientist's house, when I start the game again, the punching gloves will not appear. But if I use up all my stars when starting a new run, the gloves will appear for that run. No more energy to try more runs...
Other things noticed:
1) On new run, if I buy the slingshot upgrade (not sure what to call these), I can't break pots and still have to buy slingshot from crafter
2) On the new run upgrade screen, the top right UI overlaps a bit on the top right upgrades
3) Still on the new run upgrade screen, if i get the 8* seed bag upgrade then 2* shoes, 2* stick, 3* key, 1* fish, the top 2* mining upgrade appears but cannot be bought. I had to buy 4* seed bag then 5* match then I am able to buy the 2* mining upgrade. If I 5* ladder then 5* metal, I am also unable to buy the 2* mining upgrade.