I'm not entirely sure from memory, but I think the network card should NOT get its own IRQ in the BIOS for the D8B/HDR.
From what I recall, the only IRQ for ISA devices that should be reserved is 10, and somehow I'm thinking that this is for the MIDI card (quite honestly, I get confused about the insides of the D8B and HDR... it's at least for that, if it's the same as for the D8B).
Maybe for a test, remove the network card, leave the MIDI card in the slot that is labeled for it, and try like that. Could be a conflict between the network card and the MIDI card (but then it should really also only be settings, as long as both cards are original to the HDR).
If the MIDI card works after that, you could either troubleshoot where the conflict comes from, or just keep the network card removed (unless you want to copy files via FTP or cascade more than one unit... but I think most get their files off of the HDR in another way (e.g. remove the drive caddy and connect to the computer via a IDE/USB adapter).
Generally, though... if the BIOS is set right, you usually don't have to deal with any "other" IRQ conflicts, like you might otherwise have to when running Windows on similar hardware.
Depending on the MIDI card (i.e. if it's the "Midiman" type), you might also have to set jumpers on the MIDI card, to make sure the IRQ and base address match... but D8B/HDR users usually don't have to mess with this, so it's unlikely that this got changed away from the default... but it would be worth to check.
There's an article about DIO8 firmware revisions and their changes somewhere in the database... I believe version 2.0 also has the correct/normal phase for its ADAT ports... but I think 2.0 wasn't setting the 90 degree offset for DA38/DA88 recorders correctly. So, if you're clocking the HDR off of one of the 2.0 cards in the D8B, that might actually give the "regular" word clock, so it might help to get around having to use an Apogee clock card.
That the phase on the DIO8 2.0 cards isn't at 90 degrees, is a bug, from what I understand. But it would work in your favor, in this case.
I only read about all of this, btw., because I recently wired up an HDR to my D8B via TDIF cables (and have my DAW computer connected via ADAT cables... and can switch in the D8B, which one I want to have interface with the D8B... selectable in banks of 8).
I had all kinds of trouble, and learned from the database, that the sending and receiving DIO8 cards should always have the same firmware number.
I always thought I should put the same firmware number in the same device (e.g. 3x2.1 in D8b and 3x2.0 in HDR), but that was what caused the issues with TDIF I saw.
So, apparently it's best, if using mixed such cards, to use, for example, DIOv2.0 in Bank 1 in the D8B and the HDR and/or DIOv2.1 in Bank 2 of the D8B/HDR, etc... so that the sending and receiving device always have the same firmware version.
This might only really be relevant when using the TDIF ports, though. When NOT doing it was described above, I got crazy frozen meters und the D8B would freeze after a few seconds. I happened to have a total of 6 v2.1 DIO8 cards, and put them in both, the D8B and HDR, and the problems stopped. So, this "might" be something to look out for, but is likely not as important for the ADAT ports as for the TDIF ports.
Ausserdem... Mariechen klingt ziemlich Deutsch. Wir koennen also auch gerne auf Deutsch umschalten, falls das leichter sein sollte