Right, taken my time in responding as I wanted to observe the issues over time. And I have come up with... very little. The basics are all covered (history deleted, reset transformations etc. It happens on occasions and only on conversion. If I go straight to .dae it works fine, if I have to go through the .fbx converter, that's, if ever, where the problem is. I can only assume that yes, it is down to bad geometry (crossing planes with reversed normals etc) that a straight to .dae pipeline handles, but an fbx conversion picks up on.
Either way, it is not a deal breaker for me in any way, just a glitch that I work around by redressing my object usually. Sometime "smooth" helps, though rarely.
Thanks for everyone's input. Will update if I find out more.