Hi Andrew,
Yes the effect of atmospheric dispersion (particularly if combined with CA) is well known in amateur spectra too eg
http://www.astrosurf.com/buil/dispersion/atmo.htm
but that does not seem to explain this case where the results were ok when the seeing was better, unless the target was also higher in the sky or the location was such that the parallactic angle fortuitously aligned better with the slit
Cheers
Robin