I have a preconfigured NLE PC specifically built/bought for editing from a specialist NLE company and all the drives are connected as yours and I've never had any problems with dropped frames.
I would suggest you get a drive testing programme. I think Pinnacle have a free download of one on their web site. If not try one of the disk companies such as Maxtor or other editing software companies.
Make sure that DMA is enabled for both drives. Make sure the editing prog is setup to use the capture drive for the scratch disk (temp area for video files etc).
Try replacing the IDE cable. Make sure the replacement is a full spec UDMA cable and not a cheaper IDE cable designed for a CD-ROM drive. I've seen it recommended that you
don't use cable detect.
Few things to try then
Good luck,
Mark.