How did you measure the expression? mRNA or protein level? If protein level: Soluble or whole lysate?

here are a few things that I want to know:

the expression of a fusion protein depends upon the way it folds. so for few proteins the tag is kept on N terminal whereas in others  the C terminal tag is preferred. the tag should not affect the protein expression. that is why if the catalytic domain is at the N terminal, the tag is put at the c terminal. same concept is followed for proteins containing coiled coil domains, as coiled coil domains is responsible for protein- protein interaction.  

good luck

Although fusion tags rarely affect transcription, in protein expression and accumulation level the position of protein fusion tags do affect the protein expression (accumulation). in the case your target protein is not very stable in the expression host, the GFP at the N-terminus will help your protein folding after translation (proper folded GFP enhance chaperones to fold the target protein) resulting a higher protein expression (accumulation) level. In compare to that with an N-terminal GFP tag, the folding of a fusion protein with a C-ter GFP tag is initiated with the target protein, any misfolding of the target protein (in most cases it is more difficulty to fold than GFP) will lead to protein degradation/insoluble expression, and as a result, it has no effect on the target protein expression/accumulation level.