it is difficult to measure the 5 uA using a VOM.

I think you are on the right track.

Check all the grounds
This means the controller ground to the AC supply and ALSO the furnace chassis ground to the AC supply.

Check that the flame sensor insulator is clean so that there is no partial short to ground of the flame sensor output whick is a very small DC voltage or current realtive to funrace chassis ground.

Check that the flame sensor probe is not very dirty but I don't see how that would casue the original symptom, but culd casue the symptoms you have now.

Check that the flame sensor probe does not touch metal but is properly touching the flame.

The flame sensor probe acts as a tiny battery and the controller needs to sense that current. THe flame sensor current is relative to the furnce ground which needs to be connectd to the AC ground and to the controller ground.. I guess also make sure the burner jets are also grounded to the chassis. The flame is grounded to the burner jets actually.

Mark