possible error in cufflinks?

[dnusol]

Hi, after running cufflinks and cuffcompare on my arabidopsis experiment, I think I found some inconsistencies between the combined.gtf file and the sample.tmap generated. The Cufflinks gene id does not match across the two files. See this example:

grep -w 'MEE4' transcripts.tmap 
MEE4    AT1G04630.1     c       CUFF.1011       CUFF.1011.1     100     194.737485      166.827810      222.647159      91.465400       841     CUFF.1011.1

grep -w 'MEE4' cuffcom-out-all-sinG.combined.gtf 
Chr1    Cufflinks       exon    1289694 1290223 .       -       .       gene_id "XLOC_026901"; transcript_id "TCONS_00084569"; exon_number "1"; gene_name "MEE4"; oId "CUFF.993.1"; nearest_ref "AT1G04630.1"; class_code "c"; tss_id "TSS36322";
Chr1    Cufflinks       exon    1290772 1291077 .       -       .       gene_id "XLOC_026901"; transcript_id "TCONS_00084569"; exon_number "2"; gene_name "MEE4"; oId "CUFF.993.1"; nearest_ref "AT1G04630.1"; class_code "c"; tss_id "TSS36322";
Chr1    Cufflinks       exon    1289715 1290065 .       -       .       gene_id "XLOC_026901"; transcript_id "TCONS_00094944"; exon_number "1"; gene_name "MEE4"; oId "CUFF.1007.1"; nearest_ref "AT1G04630.1"; class_code "="; tss_id "TSS36322";
Chr1    Cufflinks       exon    1290152 1290223 .       -       .       gene_id "XLOC_026901"; transcript_id "TCONS_00094944"; exon_number "2"; gene_name "MEE4"; oId "CUFF.1007.1"; nearest_ref "AT1G04630.1"; class_code "="; tss_id "TSS36322";
Chr1    Cufflinks       exon    1290772 1291089 .       -       .       gene_id "XLOC_026901"; transcript_id "TCONS_00094944"; exon_number "3"; gene_name "MEE4"; oId "CUFF.1007.1"; nearest_ref "AT1G04630.1"; class_code "="; tss_id "TSS36322";

Has anyone seen this before? I have not checked all the way through the files but it also happens in another gene I looke for

I am using cufflinks 0.9.2

Thanks,

Dave