It is not unusual for the Active Directory database, Ntds.dit, to be sized differently on different domain controllers. When replication occurs, the DATA is replicated, NOT the DATABASE.
A number of factors govern the size of the Active Directory database:
1. The sate of database fragmentation, see tip 2635 » How do I defragment the Active Directory database?
2. A global catalog server contains data about every object in the forest, so its' Ntdis.dit could be much larger, specially in a multi-domain forest.
3. The NTFS file system only reports the size of a file when it is opened. If you have added many objects to the active directory, and replication has occurred, and you restarted a domain controller, it's freshly opened Ntdis.dat will be larger than its' peers. If you want accurate database size information, set the Garbage Collection data value to to 1.