This sounds like the usual problem where the format ID does not match the original one. This is not stored in a D64 file and is lost and breaks many multi-disk games that look at the format ID to tell what disk is inserted.
Do a directory of each disk, note the format ID (after the disk name).
Format each of your disks first on your drive with this ID, THEN transfer the D64 to it.
It should fix the problem.