I had this problem and it seemed to come from two sources:
1) if you raise the roof and then pause the action halfway, it exposes a rubber bump stop on the black panel that would ordinarily be called the parcel shelf. The rubber bump stop can be screwed up or down. If it is too far down, the parcel shelf creaks
2) also, if you raise the roof and pause it halfway, it exposes all the roof rubbers. Wipe some glycerine (glycerol) on the all rubbers. Glycerine is a lubricant that rejuvinates rubbers.
These two fixes seemed to work for me.