If you have been eating it for ages, then it should not be food allergy. But still, one may have delayed hypersensitivity.
Are you eating squash that is cleaned and cut and/or cooked at home
Squash that is precut and taken raw can cause food poisoning if it is Infected either due to contaminated water or food handlers poor hand hygeine
Next Steps
try boiling or steaming some squash and eat and see if you still have the problem
Health Tips
stool routine microscopy examination is advisable when you have squash associated diarrhea