I have this problem too. Really annoying! I've looked through every single post and page and I am not using these fields on any of them.
I looked through the dump of my database and found that CF7 creates posts with those custom fields inserted. These posts are somehow hidden from the post lists, but it is there. Look at the code used to insert the form:
[contact-form-7 id="339" title="Contact form 1"]
That id field is the id of the post, and it holds the custom fields. Since there is a post that uses those custom fields, it will show up on the suggestion list for all other posts. This is stupid and intrusive. Bad solution. This compounded with the fact that this plugin creates an entirely new top-level section in the admin page (next to 'Posts', 'Pages' etc) instead of creating a page under 'Settings' like all other plugins, make me uninstall this.
When you do, make sure that you delete all your contact forms first from the CF7 admin page. This should fix it.