An IDE chain requires a device at the end of the chain to maintain the required impedances (to minimise signal reflection). The caddy, I'm assuming, is just a dumb connection to the HDD, rather than intergrated electronics /etc.
In this case, if the HDD is not installed, the chain isn't properly terminated and it may cause data/signalling errors for the slave DVD writer. On top of that, the Master is responsible for controlling the channel, and while often the slave will still work, many won't - especially at higher speeds like UDMA33-66.
In either of these cases, god knows what information is being received by the controller. Technically the controller should be controlling where everything is going, when using DMA mode, so it shouldn't cause issues wih other devices or conflicts in the RAM. But there may be bugs with drivers which have never come to light except when vista fires up, loads generic drivers & cops corrupted data/instructions from the optical drive.
As far as the Vista install goes, if the drives were disconnected when it was installed, vista cannot destroy the data on them (obviously).
The potential for corruption occurs at the following points though:
A) When you disconnected them, you have stored them next to a magnetic source which affected the drives (possible but unlikely) like your CRT monitor.
b) When you reconnected the two PATA drives to the motherboard, you have inadvertantly connected them to the wrong chains & have set the access methods & size manually, or the bios has either "AUTO" redetected them and has used a different method to access them (CHS / LBA / LARGE) ,and when read has corrupted the mbr/FAT in ram only .. which makes it look like the drives are blank.
In any case, so long as you don't perform any writing operations on the drives, the data should still be there, you just need to try the different access methods & ensure you have the correct sizes detected.
The last thing is possibly the IDE cables have been damaged when you've disconnected/reconnected them .. replacement of them should fix the issue.
So summary .. to try:
Caddy/HDD is to be master & is to be the only device on that IDE chain.
Replace the IDE Cables (no round cables).
Re-Detect the Drives in the BIOS (autodetect) for the size, then manually try LBA/LARGE/CHS ... do NOT write to the HDD's until you have verified the correct method .. for a few days
Check if you can download updated Vista drivers for your IDE controller.
And worst case scenario ... run a memory checking utility to thrash your RAM and check that it's not the cause of the issues. It's a common problem which goes unnoticed and you don't realise it until you lose something.