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Stopping the loading may work - it there is no other activity going on then you should be OK.
If you want to guarantee the undo doesn't get overwritten for the length of the export you can run switch on guarantee undo retention for the undo tablespace - by default it is just a target not a guarantee - see this link for more details:
If you are using the same script them it must just be down to contention somewhere between the computing resources - the main thing affecting the speed ti probably the i/o speed - are you using a shared SAN and a shared disk array - perhaps other servers/databases are using up resources and taking them away form the export?