This is a known bug in Poly UV editing. The way to fix this is to do your tweeks on the UVs until you are happy. Then select your model in object mode and go to Edit Polygons/Move Component Tool then without doing anything select the object mode again. Lastly delete the meshes construction history. This will save the UV information for your mesh safely. Best to save your scene after this too.
If you use the script editor to trace these steps, you can create a Mel button that does this process for you. I have included the mel script that I use below that will effectively do this for you below.
MovePolygonComponent; // turn on the move poly component tool to add a layer of non-UV history //
changeSelectMode -object; // turn the selection mode back to object //
delete -ch; // deletes the construction history of the selected objects //
simply copy this to your current shelf to make it a Mel script.
Hope this helps,
Morris