I understand that this thread is a few months old, but I have some new and relevant information to add.
I experienced this issue with multiple later Voodoo cards on my Athlon-XP machine, using the KT133A chipset. Today, I read through the datasheet and discovered this PCI register:
Device 1 Offset 40 - CPU-to-AGP Flow Control 1 (00h)RW
7 CPU-AGP Post Write
With my 5500, there is no replacement BIOS that I have found to solve the issue. However! By using PCISET I was able to disable this register:
PCISET 8305 1106 40 10000000 00000000
And now there is no flickering on the 5500 in the Duke3D title screen. Something to try if you don't fancy flashing a BIOS.