Short version, there's an issue with item fx and melda plugins in that if you move an item with an fx to a different track and then undo, you'll lose the settings of the fx and it resets to default. The fix is to disable 'save minimal undo states', but this must be done on each instance, rather than in the FX browser. Apparently melda asked for it to function this way (i'm sure they had their reasons but this has seriously screwed me this week, lost about a whole day's work in total).

Disable this
Here's the thread on the reaper forum:
http://forum.cockos.com/showthread.php? ... ost1758785
Just wanted to shine a light on this to avoid others getting hit by this.
Thanks