David - I haven't had your issue, but did have the issue of major lag when switching between cameras. So much so that I used to fire off a dummy exposure just to wake the camera up, then pause about 5s, then start the sequence! No idea why that is the case. Possibly the situation is worsened by having the low-end DSLRs like you do (and I did in the past).
Phil - if you are desperate, you should join & post to the SEML (Solar Eclipse Mailing List). I don't recall too many posts about EO specifics in the past, but there is likely a lot more people on that group who use it than there are on IIS.
See:
http://www.mreclipse.com/Special/SENLinfo.htm