Proliant ML310 & ML350 Servers & Chkdsk

[CA1140313]

Has anyone experienced problems when chkdsk runs on bootup to windows and it can take hours to complete and launch into Windows?
ML310 servers are configured with dual 40 or 80gb ATA100 disks confirgured as RAID1 and ML350 servers have a RAID 5 set of 36gb or 72gb disks.
When chkdsk runs it often stops at Stage 3 100% then after a long time moves on. Unfortunately with mission critical servers being down for 5 hours is not ideal.
Investigation on other support sites suggests that this can be the case but i was wondering if it is a known problem with Proliant servers and if there is a fix or potential upgrades which can cure the problem.
Any help much appreciated.