Duplicated genes and genome fragmentation
The tBlastn looks good and looks like some sort of parology, although the hits you are getting need to be checked to make sure they are not psuedo-genes. The shot-gun genome however appears poorly annotated because it had misannotated 5-1 and 5-2. What I don't understand is why you haven't performed a blast back over the original highly annotated genome? You must have done this?

There are a few avenues to go down here, what I'd like to know which group of protists are you working with? I don't need to know the species, but I do need to know the family please.