Hi Yazhu,
I don't believe we've tried any Precision 690's in house, or for that matter any systems with the new Intel 5000X chipset that model has, but I'd be very suprised if you had any issues running the PCIe-1429 (a x4 card) on the PCIe slots on that system. The specs say it has three x8 physical/x4 wired slots, so there's not any up/down conversion necessary. To my knowledge there have been no issues on any of the newer Intel-based chipsets in the last year or two when running an x4 card in an x4 slot. Mostly the problems that still occur are when trying to up/down-plug cards, and even then its usually only on buggier BIOSes.
Another option for a system would be a Precision 390. We have plenty of these in-house and they work fine with our PCIe IMAQ boards. You can get these configured with up to quad-core Core2 processors, so there's not much difference in processing power between that and the Xeon-based Precision 690 (unless you were to add a 2nd quad-core processor to the 690). The 690 can support more memory, and at least on paper can get more memory bandwidth with that new chipset's memory architecture, but this may not make much difference depending on your application (I also haven't seen benchmarks of this chipset yet). Of course you also get more slots and beefier power supplies in the 690, but you also pay a premium for them. If you're not going to customize the 690 with all the maximum beefy options that aren't available on the 390, there probably isn't much benefit to that over something like the 390 (just my opinion).
Hope this helps,
-Eric G
