I finally had an opportunity to run these two together for the first time last night and was very saddened by the horrible reality of constant loss of samples. I thought I had gone and set up the Vaio to avoid this, but apparently not! I'm running a Vaio VGN S360 (Pentium M 1.7 GHz 512 MB) which does have a TI firewire host controler and a Fujitsu drive which is only 4200 rpm, but I thought it would at least handle the two tracks OK.
After going through and double checking the adjustments to my computer I am starting to think it is the drive that is at the root of my troubles, yes, I know,I am planning to get a 7200 but this was a last minute request to record.
I have gone through and tried the lowest to highest samples per buffer settings, changing sample rates and bit rates and it is still very apparent, though some changes did produce more drastic drops.
At this point I am planning on an external drive and the addition of a 512MB memory stick, but if anyone has any other suggestions I am all ears.