It sounds like you moved the IRA by distribution and rollover, not by nonreportable trustee-to-trustee transfer (or at least that's what the original IRA custodian is claiming by issuing a Form 1099-R). If that's the case, the RMD was satisfied by the distribution from the original account and only the amount distributed beyond the RMD was eligible for rollover. If the entire amount was rolled over, the portion that was RMD must be treated as an excess contribution to the new IRA to the extent that it exceeds the amount that you are eligible to have contributed as an ordinary IRA contribution. With the RMD already satisfied by the distribution from the original IRA, the distribution from the second IRA was an extra distribution (or actually should have been distributed as a nontaxable return of contribution, but the new IRA custodian would have no idea that that was necessary unless you requested such a distribution.)
