some odd out put in combined GTF RNA-seq Cufflink

[honey]

I am using the most recent version of Cufflink and has used the previous version of same tool for RNA-seq analysis. After updating new version I ran few RNA-seq analysis and have noted one strange point in combined GTF files out put;
In column old cufflink Ids there are few entries which are repeated for Ensembl transcript ids meaning same Ensembl transcript id is put in two columns one under olds cufflink id and second under Ensembl transcript id. There are lot of such entries. I was wondering if someone else have experienced the same pattern or I messed up something? ( I think I am not)
Old cufflink ids used to be unique per row, then in this scenario how should be interpret? I checked these ENST repeated entries back into Ensembl they are not unidentified and are well defined?

Thanks for your input