That fact that you have a Form 5498 with an amount in box 2 but no Form 1099-R reporting a distribution means that the original IRA custodian believed that they were doing a nonreportable trustee-to-trustee transfer but the receiving custodian believed, probably mistakenly, that they were receiving a rollover. A actual trustee-to-trustee transfer is not reportable on either Form 1099-R or on Form 5498. If the funds were never paid to you personally but were instead paid to the new IRA custodian for your benefit, the new IRA custodian was incorrect to record this as a rollover.
