Buffered IDE Interface and IdeFix

[mfilos]

Where have you connected the 40pin CD-ROM? Into Primary or Secondary channel?
In primary it will fail since the 44pin and 40pin header share with each other.

Only way for it to work are either:
1. using HD in Primary as Master, and CD-ROM as Primary Slave (slave is the only one used anyway in slim JAE-->40pin adapters unless you got a rare adapter that has jumpers on it). That ofc required an 3way IDE cable (with proper adapters for 44-->40 and vice versa)
2. using it in Secondary channel (master or slave doesn't matter I think). That way you'll have HD SCSI ID = 0, and CD-ROM SCSI ID= 3 (if set to slave by default).

In 1st case you don't need IDEfix since OS3.9 works just fine in Primary channel without it (for secondary channel i think IDEfix is still needed but might be wrong)

[mfilos]

If I connect the hd to primary 44 pin header, and the cd-rom to primary 40 header, it wont boot from hd, just goes to the "insert disk screen". And the activity light on the IDE->CF adapter keeps on all the time?

Apparently you haven't read what I wrote at all mate...
Since you're using the 1st of the option I said...

1. using HD in Primary as Master, and CD-ROM as Primary Slave (slave is the only one used anyway in slim JAE-->40pin adapters unless you got a rare adapter that has jumpers on it). That ofc required an 3way IDE cable (with proper adapters for 44-->40 and vice versa)

That means that you just CAN'T use BOTH the 44pin Primary header and the 40pin Primary header since they're both the same thing! If you want to use only the Primary channel (44 OR 40 - not both) you need to use a 3way cable (3 female IDE connectors) setting HD as Master and CDROM as Slave. I repeat... You CAN'T use both 44pin and 40pin header for primary channel. Only the 44pin OR 40pin from Primary channel AND the 40pin from the Secondary channel

If you use the second method... (HD on 44pin or 40pin Primary header and CDROM on 40pin Secondary header) then you either need the IDEfix97 installed or the atapi.device as Thomas said

[mfilos]

LOL @ rude

Anyway, cheers and hope that you'll fix it and have a great time

[mfilos]

CDROM never show's up in the Early Startup Menu mate. Best way to see if it works, is testing it with an OS3.9 Emergency disk

Don't worry if you connected everything just fine, just do what you do, run IDEfix and you'll be set

[mfilos]

:O I didn't know about that my friend. Are you sure? (there are several 4way buffered adapters) so I kinda thought that the header was outside a circuit (like an extension 1-1 apart from the 4 power pins)!
That would be awesome mate if it's true. I'll give it a try also.

Cheers Thomas