GTF sorted crash - not finding/using existing sorted GTF

I've tried this with two .gtf files and got the same result with both. Both GTF files were obtained from iGenomes. I got the error first using an unsorted GTF, so I tried sorting the GTF first, the sort completes without error, but flux doesn't recognize the GTF as sorted and tries to sort again and crashes.

I sort the .gtf first with:
flux-simulator -t sortGTF -i genes.gtf -o genes_sorted.gtf
Flux-Simulator v1.2.1 (Flux Library: 1.22)

[SORT] Sorting /Data/Software/flux-simulator-1.2.1/bin/genes.gtf to /Data/Software/flux-simulator-1.2.1/bin/genes_sorted.gtf
Sorting genes.gtf sorting GTF file OK (00:00:34)
OK (00:00:34)

Then I set up my parameter file (test.par):
REF_FILE_NAME genes_sorted.gtf

Then I run flux-simulator:
flux-simulator -p test.par
Flux-Simulator v1.2.1 (Flux Library: 1.22)

[INFO] No mode selected, executing the full pipeline (-x -l -s)
[INFO] I am collecting information on the run.

[INFO] Checking GTF file
Checking GTF *[WARN] Unsorted in line 939 transcript id NM_001033581.1 used twice, on: 1,1
[GTF FILE] The GTF reference file given is not sorted, sorting it right now...
sorting GTF file OK (00:00:29)
[GTF FILE] The Simulator will use /Data/Software/flux-simulator-1.2.1/bin/genes_sorted_sorted.gtf
[GTF FILE] You might want to update your parameters file
[PROFILING] I am assigning the expression profile
Checking GTF *[WARN] Unsorted in line 939 transcript id NM_001033581.1 used twice, on: 1,1

[ERROR] The reference annotation GTF is not sorted!
java.lang.RuntimeException: The reference annotation GTF is not sorted!
at barna.flux.simulator.Profiler.createGTFReader(Profiler.java:756)
at barna.flux.simulator.Profiler.readAnnotation(Profiler.java:202)
at barna.flux.simulator.Profiler.call(Profiler.java:127)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:429)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:198)