What exactly do you mean by "imap id"? If you mean the UniqueId property, two emails having the same unique ID in a single folder would indicate a serious bug in either the IMAP server or client.
Please create a communication log using
Imap object's LogWriter property that includes a listing of a folder with those two messages. This should make it possible to tell what is going on. You can post the log here or mail it to email@example.com for analysis.