What filter?

When you go under tools message and then click on create message from. I use it to send messages I don't want to receive to my junk folder.

Go to Tools > Message filters. Just how many filters do you have (each of those has to run on every email you receive so the receive overhead is quite extensive is my guess.

You view the messages by looking in the junk folder obviously as you specify that location.

see also https://support.mozilla.org/en-US/kb/thunderbird-and-junk-spam-messages and http://kb.mozillazine.org/Junk_Mail_Controls