I don't know if there are multiple versions of Yoomp! floating around, but the XEX I have has always worked, as does the ATR. Make sure BASIC is disabled in the loader options, since leaving it on can create problems with many titles.
By transmission errors I mean hardware glitches, effectively, which are the only things that can account for issues whose behaviour is apparently random. I wouldn't expect too many cards to be unstable with a SIDE2, however, so you may be looking at some other gremlin. Check the BASIC setting first.
Mr Flashjazzcat, you are a legend :-) Switched off basic on the SIDE2 Loader and all the images which did not work before now work :-) I am off to play some Yoomp and dropzone :-)