Trying to invoke:
Set-MsmqQueueManager -JournalQuota 5000 -MsgLogStore 'D:\logs\MSMQ' -TransactionLogStore 'D:\logs\MSMQ' -MsgStore 'D:\logs\MSMQ' -Confirm:$false
This command modifies registry data and tries to restart msmq service but this service is not getting up.
Restoring registry data back to default fixes problem
I think this is because setting storage directories should be done with few other operations but this command doesn't execute them. It only modifies registry.
Modifying registry manually gives the same result (msmq service is not starting)
Setting journalquota and msglogstore only works, adding transactionlogstore or msgstore breaks msmq service