I don't think it would necessarily be bad to just wait occasionally. But to just wait all the time? It could look bad to your boss, but it could also - bluntly - get boring for you.
On the one hand, waiting means that you will have a percentage of downtime every day, and it isn't time that can be easily allocated to other tasks because of the scattered nature of this downtime. There is also the issue of managing client (co-worker/superior) expectations: if a task takes you five minutes of focussed effort, but that five minutes is broken by a fifteen-minute period waiting on the processing, you can't tell people that the task takes only five minutes or you could wind up on the road to burnout-from-overwork. There's also the issue of what happens on those rare occasions when something goes wrong with a task, you come back to it, and the task has to be restarted.
On the other hand, if some task has an extremely low probability of failure and you don't have to watch that particular pot boiling, you can easily work on other short tasks (checking the email queues is a biggie, at least for me) while those "background" tasks are going on. This lets you stay ahead of things without trying to overbalance your own plate, and it will require you to be familiar enough with each task that you can take a fairly good guess at whether or not it will require close attention and possible operator intervention.
The trick will be finding the balance that works for you, uses your time as efficiently and effectively as possible (ie, NOT cramming it chock full of stuff to do, because sometimes five minutes of mental downtime can boost a day's productivity more than reading an answering just two more emails) and gives the client what they expect/need.