Cufflinks, cuffmerge and strandedness

[Mike2188]

I have a question, I am currently using cufflinks for multiple bam to generate .gtfs and cuffmerge on these to improve an already existing annotation (Brassica napus). I find, in several hundred instances, that I get the 'x' transcript code, which implies that exons overlap on the other strand. My data is not stranded. When I put this into genome browsers, I see the 'new transcript' is most likely an alternate transcript of the other genes. Anyway to prevent this from happening? Please see picture below.

Top are my alignments, quite high coverage

Bottom is the original annotation, above that is an additional transcript identified with code (x).

Thanks for the help!