topse, now this is a real bummer ...
there is a new FW 800 chip on the market from Agere, which seems to be incompatible (not only) to RMEs FireWire audio, and requires workarounds for successful operation.
The reason Apple used this chip instead of the former TI solution is easy to find: half the price and a lot smaller. So it is not astonishing that this chip now also begins to show up on Windows computers. We got our hands on a PCIe FireWire 800 card from Unibrain using this chip, and found the exact (!) same problems under Windows as under Mac OS X using this card.
i know (and have posted this already) that there is really much crap on the market for FW expansion cards, but again it seems apple has given up its credo to use only first class components for their hardware ... now i'm starting to understand why the maxtor oneTouch II works so unreliable on newer macs....
eg. the (also mentioned) unibrain products are totally useless from my experience and i regulary notice performance issues with VIA chips.
i've also posted earlier a link to an informative articel about FW incompatibilities http://www.rme-audio.com/english/techinfo/fw800alert.htm
have you checked your iMac is using this chip and i don't understand the *no second firewire port on the harddisk* ... as i've read it they suggest to add an additional FW-controller to the computer (a PCIe34 expansion in the given example, mainly intended for proBooks obviously)
the thread you linked to is also a goldmine for windows (the theysicon links there, a company which really knows what they are doing) although it also states that OS X system information does not provide the correct information about the used chips (if this is true, again a bummer)
some option maybe worth to try comes into my mind (since everything reads like a collison between asynchronous and isichronous mode might be involved) ... try to daisychain your devices the other way around (computer - harddisk - audio vs. computer - audio - harddisk) or given you have a FW controller on the computer with 2 ports connect them both directly (firewire devices work by design like hubs - 1 in, 2 out, 1 for the device), possibly protocol issues can be avoided in one configuration.
heading the NAMM we are a little bit short in time currently but i'll try to organize a double check on our intel Imac (please provide harddisk model to allow a very similar setup)
christian
and remember: only a CRAY can run an endless loop in just three seconds.