MSI K8NGM2-L and MSI RX1650XT-T2D256EZ incompatibility???

This topic is also posted in the VGA forums
Full specs:
MB: MSI K8NGM2-L http://www.msi.com.tw/program/products/mainboard/mbd/pro_mbd_detail.php?UID=702
VGA: MSI RX1650XT-T2D256EZ http://www.msi.com.tw/program/products/vga/vga/pro_vga_detail.php?UID=780
CPU: A64 3200+ Venice (used it for 2 years with no issues myself)
Cooler: Arctic Cooling Alpine64
RAM: Corsair DDR400 1GB (2x512) Value Select kit (used it for 2 years with no issues myself)
HDD: Maxtor 80GB PATA (used it for 1 year with no issues myself)
DVD: NEC 7070SA
Card reader: Chieftec 25in1 3,5"
PSU1: Bestec 350W, 2x 12V @ 18A each (Came with the Asus TM-211 case)
PSU2: Enermax Liberty 400W, 2x 12V @ 20A each (used it for 2 years with no issues myself) http://www.enermax.com.tw/english/product_Display1.asp?PrID=7
I just built a new PC for my sister based on the MSI K8NGM2-L mobo. We chose it for the small size and never really planned to use the onboard VGA. After the system was built I borrowed a HIS Radeon 1650XT iSilence2 VGA http://www.hisdigital.com/html/product_ov.php?id=269&view=yes and tested the system with this. It took 2 times 8 hours (2 nights) simultaneous Prime95 and 3DMark 2001 looped testing without  a problem,  but since I did not want to loose the PCI slots to the HIS card's passive cooler, I decided to buy an MSI RX1650XT-T2D256EZ instead which is passive too, but has the fins on the top side.
Upon starting up the system for the first time with the MSI VGA, there was no video signal on either of the card's 2 DVI outputs. The card also did not function in another PC so I took it back to the store and they exchanged it.
The second RX1650XT did the same thing, except it appeared to be "working". I heard the correct BIOS POST-beep, the hdd led flashed and the computer appeared to boot into XP. Upon allowing the onboard VGA to function simultaneously and connecting the monitor to the Geforce 6100's output, it became clear, that the PC does get to Windows, which even recognizes the 1650XT as new hardware - still no video signal on that card.
Things I've tested:
- changed the case's PSU (350W generic Bestec with 2x 18A 12V) to an Enermax Liberty 400W
- disconnected internal USB card reader I bought and installed at the same time as the first MSi 1650XT
- disabled all USB in the bios
- reseted BIOS
- loaded Failsafe BIOS settings
- updated the MB BIOS
- tried 3 different monitors - 1 CRT and 2 LCDs, all analogue, with the DVI-I to VGA adapter(s) supplied
I also took the whole system to the store I bought the MSI VGA at. They tested it for  about 40 minutes with the following results (with the original Bestec PSU, mind you!!!)
- The MSI K8NGM2-L motherboard worked with every PCIe VGA they through at it, except for my MSI RX1650XT-T2D256EZ.
- The MSI RX1650XT-T2D256EZ VGA worked in every MB they used except for my MSI K8NGM2-L.
Any ideas?

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