@Cliffowrms, come to think of it, it does happen when I am asking multiple NPC's where a location or person is, so it could be that 'too many clicks'.
As to front ends going wrong; there is nothing that can go wrong. All they do is allow you to create a dosbox conf file through a windows front end of tab, left click,etc. Once this conf is set up, the front end puts a copy in the game folder. When you start the game from the front end it starts DOSBox that uses that conf file. At that point only DOSBox is running. The front end has done it's job. When I double click on Daggerfall in my front end, it is exactly the same as clicking on a DOSBox shortcut.
As to saving every 5 seconds, you'd think DOSBox could come up with a key combination to save the whole game code at that point. Sure, that might mean 60-100mb save files, which for DOS is a lot, but for games in general it's not! I have the feeling if that 'auto save' existed, we would remember to save more often! It wouldn't be difficult to save straight after the autosave, and on finishing the game for that period, just going to the Daggerfall folder and deleting that 100mb autosave - so it would only be there temporarily!