I am having a really odd and frustrating issue with 2010; when I freeze a layer in a specific viewport the layer sometimes (but not always) gets switched off, so the layer is not viewable in any viewport as it does not get switched back on unless I notice and turn it on manually.Anyone had this problem before?

Check your settings within LayFrz.eg.Command: layfrzCurrent settings: Viewports=Vpfreeze, Block nesting level=BlockSelect an object on the layer to be frozen or [Settings/Undo]:

All set up as it should be; the offending layers are not frozen, they are turned off, which as far as I can tell isn't a sytem variable.

Oops, did you check LayOff for the same thing?

I think that has sorted it, thank you very much.

Welcome. :)