Disappearing layer in aftereffects

Half way through making the logos creative I noticed that on some of the photos the logo started to disappear. I looked on the Internet ‘disappearing layer in after effects’ and some answers were because the logo is a png file although my other png logos are working. http://forums.adobe.com/thread/783940

After doing more research on the Internet I didn’t find any results. I decided to take the png file and opened it into Photoshop to convert it into a jpeg and Photoshop file. My teacher did do some research also and it said that the png files wont disappear if they have alpha channels switch on with is done while saving the png photo in Photoshop but unfortunately I couldn’t do this nor could I do this on any other file type. Instead I put the new photoshop file logo into my ident, when switching it to 3d on the photos it disappeared so I’ve kept it 2d and have started to make the logos move.