I choose an AGP card because my previous ATI 9800 is dead.
My motherboard + ram + CPU works well, I don't want to change all my hardware just for a graphic card.
You may have few options to NOT be doing that. AGP cards are about a year or so from being pulled completely from the market. As a bus, it's "okay" but the PCI-E interface is better overall and everything in creation has went to it. You're going to find that while your hardware is working, unless you want to go with older tech, the AGP motherboard is a liability.
AMD's edge bridge, the Rialto, has had issues with Linux operation for a while now on their proprietary driver. NVidia's got decent AGP parts but they compare more with the R500 parts in performance and ability- not the same as the R600 you've bought and having problems with.
Right now, there's several options to you:
Ride it out, hoping that AMD gets their act together or the FOSS crowd beats them to it. You may be waiting a long while for that one.
Buy a 7800GS from BFG Tech or one of the other companies using an NVidia part (which does seem to work right on Linux and is an AGP part...)
Buy a whole new motherboard, CPU, RAM, etc. and side step the issue of a deprecated bus spec and be able to pick and choose a range of GPU options, all of which largely work.