thats a bummer Simon it was looking great, looks to me either a reaction between the stain and the clear with a fair bit of shrink back what did you use for grain filler ? going to be a prick to get it right if it was me id get hair dryer and razor blade to take the old stuff off with out using a lot off sanding and go again (i said use hair dryer as its not as hot as a heat gun) bit of a bummer but its quite fixable. your pretty clued up Simon its a to good of a kit to toss out
if there is someone who could fix it, its you