I know to be very late in the topic, but i solve all boot-problems wit EasyBCD installed under Windows. In you case I would suggest following:
1) Reset/erase all entries. Notice: Don't reboot before you have not made at leasr one Entry.
2) Setup on each HDD one MBR (Master Boot Record)
2) New bootloader (Add new Entry) for Windows on big HDD, I suppose C:\
3) New bootloader (Add new Entry) for Linux (Grub 2) on smaller HDD
It's mean you setup two MBR on two different HHD's on each one you install one bootloader.
Some motherboard (e.g. Asus p5b Deluxe) have the option to can choice the boot-HDD by pressing "F8" just after using start-button, to not be confused with windows "F8" that come alittle bit later.
In this case you can start the desidered OS by selecting HDD. On my machine works it fine.
My slogan: When life gives you lemons , make lemonade! My ConfigurationCase:
Thermaltake Soprano DS BlackPower Supply:
Thermaltake Thoughpower 850WPCB:
Asus P5B Deluxe WiFi AP SoloRAM:
4 x 2GB Kingstone DDR2 @1066 MHzCPU:
Intel(R) Core(TheeMahn)2 Quad CPU Q6700 @ 2.66GHzCD/DVD:
2 x CD/DVDW SH-S183L TSSTcorpHDD1:
4 x Hitachi DLA 380, 250GB each in RAID5 in total 750 GB (NTFS Vista Ultimate 64 Bit)HDD2:
Samsung 1TB = 500 GB (NTFS Windows Backups); 150 GB (NTFS Linux Shared); 175 GB (ext4 Linux Ultimate 2.9 64 bit); 175 GB (ext4 Linux Backups)HDD3:
Initio 200 GB Ext. USB2 (Windows Downloads)GPU:
Asus NVidia ENGTS 450 1GB GDDR5 MemonryDisplay:
Asus VE228H Full HD 22" HDMI 1920*1080 16:9Printer:
Canon PIXMA iP2700Scanner:
Canonscan LiDe 25