I fixed the problem. Eventually, after trying everything else, I deleted the .mxd and created a new one (Even though the existing .mxd was brand spanking new!) and the layers appeared. Although I don't know if this can be classed as a fix, since i don't know what caused it - a brand new .mxd that was dodgy?
I've noticed lots of other bugs with this software that has caused me to waste a lot of time. For example, trying to get data off the mobile device using the 'Synchronise Mobile Cache' tool, er, doesn't synchronise so the updates won't load into arcmap, or the mobile device won't be updated from arcmap...