I think, generally speaking, that agents are as overwhelmed as anyone else. And email is a funny thing. You send an email query or submission. It sits in a box. Then you send an email saying you have accepted representation. The agent clicks next and forgets about it. How many old emails do you have sitting waiting for action?
When it comes to hardcopies, the agent may be forgetful, or the agent may have told his or her assistant to send that one back and the assistant stuck in a form reject by habit. Or maybe the agent actually read the query even though you withdrew it and sent you his or her genuine thoughts on it, form or not, rejecting it.
I think worrying about an agent rejecting you more than once is likely not the best use of your time. Obviously this is not the agent for you. And if you really have a problem with his or her organizational abilities because he or she rejected you twice or after you withdrew the submission, then clearly you are lucky he or she is not in charge of submitting your book to publishers!
Z