Difference is that they come from different inputs. One comes from the operating system clipboard and another from the keyboard.
Password fields in the web, depending on the language (HTML, AS3, etc.) that the control was implemented can prevent passwords to be inserted from specific inputs. Also, if the control is from HTML it can be modified with JavaScript to reject any clipboard input.
If you are really into discovering what is preventing you from pasting a password, you can try loading the page without say the JavaScript code that is blocking the clipboard input into said field and see if it allows pasting. Just for fun. (Read the terms of use of the web page before. You don't want to or should mess with something forbidden).