Cuffmerge very strange errror pattern

[Helical]

I have a strange error pattern that I'm hoping someone here can shed some light on. I keep getting the following error when running cuffmerge:

Error: duplicate GFF ID 'M41013' encountered!
[FAILED]
Error: could not execute gtf_to_sam
Traceback (most recent call last):
File "/cgr/home/qh5653/cufflinks-2.0.2.Linux_x86_64/cuffmerge", line 576, in ?
sys.exit(main())
File "/cgr/home/qh5653/cufflinks-2.0.2.Linux_x86_64/cuffmerge", line 554, in main
sam_input_files = convert_gtf_to_sam(gtf_input_files)
File "/cgr/home/qh5653/cufflinks-2.0.2.Linux_x86_64/cuffmerge", line 287, in convert_gtf_to_sam
sam_out = gtf_to_sam(line)
File "/cgr/home/qh5653/cufflinks-2.0.2.Linux_x86_64/cuffmerge", line 247, in gtf_to_sam
exit(1)
TypeError: 'str' object is not callable

The strange part is, this only occurs under specific circumstances. I have two groups of transcripts.gtf files which I want to merge:

1) Generated by tophat/cufflinks using publically available reference transcripts - cuffmerge always succeeds

2) Generated by tophat/cufflinks using custom reference transcripts - cuffmerge always fails

When I look at the transcripts.gtf files generated by both these pathways, they appear identical (besides the names obviously). Yet one crashes cuffmerge and the other doesn't.

How is this possible?