(am pretty wiped at the mo, hope this makes sense and is of indirect help)
My ongoing experience with my MOTU 4Pre (fw) is uncannily simlar.
My observation IS that the "dropout is a symptom of the disconnect"(cf, Noel above).
My further observation is that there IS indeed a change in sampling rate perceived by my Motu audio console...but it is not generated by me altering a single thing in the prefs menus or importing any audio...and in fact I only became aware of it after I switched the Motu fw off and on, post "disconnect" message(..thanks Bob for inadvertently drawing my focus to this...!):
Also in common with choinga, my board also has Realtek audio...(which, post-disconnect, Windows 7 gleefully resorts to making it the default device against my wishes, yet still decides not to play regular 16/44.1 audio on);
It is when I re-enable the firewire device that I then notice(in the Motu audio console) the sample and buffer-rate has myseriously and unpromptedly changed.
I change it to match X3[tho' to be honest I was not observant and only noticed if roundtrip latency was still warm and fuzzy at 9.3ms]...we're OK again; all is jacky-dandy until then at some undetermined stage when it isn't; cycling through even one instance of Dim Pro is what seems to generate more instances of the disconnect.
Awesome stuff re the sampling rate all.
(Choinga, just for the sake of ticking boxes, my onboard Realtek audio is on a Gigabyte X79-UD3(Intel i7 4820K))
(Well, I might just squash a few komodo dragons with my 4x4 in Far Cry 3 before beddy-byes)