TS 100 No boot when Rocket Raid Card configured

I have a Rocketraid 2320 controller. With the card installed and NO raid configured I can boot to the MS server 2003 Standard cd disk. With the raid card configured I cannot boot to the CD drive.  I also installed a SATA drive (not on the raid) installed MS server 2003 standard, all is well until I configure a raid array on the Rocketraid card.
I then only get a flashing cursor and no boot. I have changed the boot order to Boot Hard 1st then Rocketraid then CD rom and all variations of those devices.  What am I missing? Thanks. Dave

Thanks Gabor, for the response.
I refered couple of answer records like AR# 34873 and AR# 34894, I monitored trn_reset_n, sys_reset_n, clock_locked, PLLLKDET and RESETDONE signals as suggested in AR# 34894.
Status as follows:
SYS_RESET_N = 1 (deasserted)
TRN_RESET_N = 0 (asserted)
CLOCK_LOCKED = 0 (deasserted)
PLLLKDET = 0 (deasserted)
RESETDONE = 0 (deasserted)
which means the transceiver PLL frequency is not within the predetermined tolerance. Is this problem related to the PCIe Jitter Attenuator I am using on the board to derive 125MHz from 100MHz system Clock.
Thanks & Regards

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