My main display is connected via HDMI and my new display is a VGA
That is probably the problem right there. The card may have three connections but there is only two RAMDAC's on it, RAMDAC - Wikipedia, the free encyclopedia
which only allows for 2 displays at a time. I think you will find that your card (and pretty much any card with 3 connections on it) is that one RAMDAC is for the DVI port and the other is for both the HDMI and VGA port, which would explain why the second monitor starts to work when you disconnect the HDMI port.
Try connecting your primary monitor to the DVI port, with the second to the VGA port and I'd bet both will work no problem