First of all make sure this is not a termination problem. You should only have the device at each end of the SCSI chain terminated.
If your adaptec card is set up to auto-terminate (dependent on ther settings on other devices) then you need to have your EMU booted before the SCSI card boots (for me this just means turning the EMU and the PC on at the same time).
If you have a hard disk or other internal device attached to the SCSI card then you should have this device terminated and the SCSI card should not be terminated.
If you have a SCSI hard disk installed in the sampler I can't remenber (off the top of my head) whether I have the sampler or the hard drive terminated (I think I recall that the EMU internal SCSI bus connects between the sampler and the outside world rather than the sampler being in the middle).
It is a tricky one as termination depends on configuration.
If you had, say, an interanl SCSI drive on your PC and nothing connected externally then both the card and the SCSI disk would be termited. If you had a sampler with an internal SCSI disk and nothing connected to the outside world then again both would be terminated. However, if you have an internal drive, scsi card, sampler and internal sampler disk just the sampler and the hard drive in your PC should be terminated.
The outcome of all this is that if you regularly change the set up then incorrect termination will provide unreliable results.
(by the way, you should also set the SCSI card up so that bios support is not activated fro the sampler.
You should also consider updating to EOS 4.x. Partly becuase it is better anyway but also that some changes have been made in the SCSI implementation. I don't think this will resolve your booting problem but it is certainly the case that an old SCSI CD_ROM and hard drive I had work with EOS 4.x and did not work with 3.x.
On a more positive note. I have three SCSI cards in my PC (2940 and 2x2905) connected to an ESI-32, E6400 (upgraded to EOSV4.10) and E6400 Ultra (EOS V4.10). I use Soudforge, WaveSurgeon, Recycle and EOS link to interface to the samplers over SCSI. I also have 5 SCSI hard disks, a CD writer, CD rom, syquest drive and data DAT connected to these various scsi chains. It all works reliably though it did take me a while to get it all working and it never did work properly under Win 95 (I now use win '98 SE though a single card, single sampler set up was fine with '95).
It is definately worth perservering SMDI operation is really useful and I use it all the time.
The description of your current problem definately suggests a problem with termination, cabling or SCSI ID (have you set the E6400 up to avoid the SCSI id of the SCSI card?, you need to do this but I can't remember what it was called on EOS 3.x).