Did anyone had a problem like this? This is really strange. My client has 2 stores, 1 for retail and one for wholesale. When I change theme to he created theme on 1st store some modules (not all) disappear in the 2nd. Same the other way, when I change theme to created one on second store some modules disappear on first store. It wouldn't be such a problem if those wasn't the important modules like user links or currency change. Did you ever saw such behaviour? Second theme was the child of first theme at first. Then I created it as a stand-alone theme and it didn't change anything.
PS version: 1.7.7.4