allocateParty creates a new party everytime you run it. So if you run your Daml Script multiple times you get different parties each time which sounds like that’s what’s been happening here: You’ve run it once via initializeUser and then once via allocateParties directly. I recommend to have initializeUser return LedgerParties and then only run that once. If you run it via daml start, you can set the --output-file flag via daml start --script-option --output-file=parties.json.
For the Alice::… part, you can allocate such parties via allocatePartyWithHint … (PartyIdHint "Alice"). The hint will be used as a prefix.