There are a lot of variables at play. Ruling out transient issues such as network performance, and load here are a couple of possible explanations:
You are getting assigned a different batch of nodes when you run an interactive job from when you use qsub.
I've seen some sites that assign a policy of 'exclusive' to the nodes that run interactive jobs and 'shared' to nodes that run queued 'qsub' jobs. If that is the case, then you will almost always see better performance on the exclusive nodes.
Another answer might be that the interactive jobs are assigned to nodes that have less network congestion.
Additionally, if you are requesting multiple nodes, and you happen to land on nodes that traverse multiple hops, then you could be seeing significant network slowdowns. The solution would be for the cluster administrator to setup nodesets.
Are you using multiple nodes for the job? How are you requesting the resources?