Holy hill, it's really strange. I have the Water room at the first floor, have a best weaponry there and all-in-perception wear. So that room became the first and last, that raiders have seen. All Int rooms according to that positioned underneath and supplied last. My egg-heads armed with only a 10mm guns but still able to wanish roaches in no time.
Try to follow that advices:
Keep searching the wastelands 4 better equipment
Dont hurry to merge 3 rooms without having enough people
Check twice, that you really exit the game in the end of session.