I’m currently attempting to perform an analysis using GOseq on the up regulated genes of a RNAseq experiment. The thing is I keep getting a plot as the one I attached here, which is the mirror image of the one you would expect. Does someone have any insights into what may cause this? 

I did the analysis for a different RNAseq data and got a similar result only this time it happened for the downregulated genes. This data is from Arabidopsis thaliana, could that be it? I don't know if this would be normal o it indicated something wrong in the analysis.

Any insights would be much appreciated.

I doubt anyone will be able to give you an explanation because it is presumably something specific to your dataset. I suggest you have to a close look at your data to determine what are the short genes (<1000bp) in your data and why 50% or more of them are DE.