I was having the same issue... My company has only Dell PCs but no half-height Dual Display PCI/PCIe cards (for this half-height case). The task was to get the onboard display and another display card to play nice.
I Google’d around to find suggestions… found this forum.
I did get it to work… but I think it had to do with the ATI Catalyst Control Center software.
I tried a few combinations of Dell video cards… and found that the ones that didn’t support the ATI Catalyst Control Center didn’t allow use of the onboard VGA…unless it was accompanied by a card that the ATI Catalyst Control Center liked. At one point I had a 4 display output if I wanted.
ATI Catalyst Control Center won’t run unless it finds compatible hardware.
In the end, I was using the ATI Radeon HD 2400 (PCIe, DVI) and the ATI Radeon Xpress 200 series (onboard, VGA). The PC I was working on was a Dell OptiPlex 320.
It was set in the BIOS for Onboard/Card as the Primary Video.