Having 640x480 both in interlaced and progressive mode in the same system is problematic with HD 5000+ cards. It can be done but it's not easy.
If you need 640x480i, then previously delete your 640x480p mode. You may need to create a different desktop mode first and set your desktop to that mode before deleting 640x480p.
Then, if you're using VMM command line, make sure to select a 15 kHz monitor preset before creating that mode. Otherwise, if you're using a trisync preset, VMM will always want to use the upper range to avoid interlace.