To be honest, I've noticed the same type of occurence. I have a flashed 9800 Pro and a regular 9000, and for most things the 9000 outperforms the 9800. Same thing with Nvidia cards, A flashed nvidia fx5200 256mb was outperformed by a standard fx5200 64mb. All of them were tested in the same G5.
MacBook Pro, 2.2GHz SR Core 2 Duo, 120GB HD, 2GB RAM, PowerMac G5, DP 2GHz, 2GB RAM, 1x500GB HD, Sonnet Tempo X4P, 2TB RAID, ATI 9650 256MB.
Loc: Florida, USA
It's the firmware. Sometimes you have to edit the ROM to the right specs of the card. For a example a mac nVidia FX 5200 128MB backup ROM was used on a PC nVidia FX 5200 256MB. It would only use 128MB of the memory even if system profile states it's 256MB. It's weird but thats how it works.
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