This happens on PM ver 4.4.3.3 on a WIN XP (SP2) MCE system...
Open Ingest, then open the variables list, e.g., to fill in "Rename..." .
Now open the IPTC Stationary Pad, leaving the Variables list open. Select a variable from the list and double-click it. It gets applied to the Ingest dialog, not the Stationary pad.
I would have expected it to be applied to the top-most window, i.e., the stationary pad since (1) you can get to the list and use it, and (2) clicking "Variables" on the stationary dialog doesn't open another list. To get around the issue, you have to close the stationary pad, close the variables list, reopen the stationary pad and reopen the variables list. It would seem to make sense to apply a selected variable to the top-most window (stationary pad in this case) since it is modal and you can't get to the ingest dialog.