net.sf.samtools.SAMFormatException: SAM validation error

When I run the capacitor with this configuration:

READ_DESCRIPTOR MATE2_SENSE
ANNOTATION_MAPPING Combined
SORT_IN_RAM false

I get the following exception:

Flux-Capacitor v1.1.1-20121030021633 (Flux Library: 1.17-20121030021633)

[PRE-CHECK] I am checking availability of the required lpsolve JNI libs.
[PRE-CHECK] * successfully loaded lpsolve JNI (version 5.5,release 0,build 14)

[CAUTION] I overwrite the output file cshl.exons.gtf.gtf, please confirm:
(Yes,No,Don't know) Yes
Scanning annotation file Checking GTF *[WARN] Unsorted in line 16 - chr/strand chr1 + already read.
[INFO] Sorting /users/cn/pprieto/soft/flux-capacitor-1.1.1-20121024021627/LID18554-LID18555_cufflinks_exons.gtf
sorting GTF file OK (00:00:12)
scanning OK (00:00:04)
[INFO] 14811 loci, 21232 transcripts, 137500 exons.
OK (00:00:04)
Scanning mapping file Exception in thread "Thread-2" net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Record 1, Read name PRESLEY:6:96:797:1150/2/1, Mapped mate should have mate reference name
at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:448)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:540)
at net.sf.samtools.BAMFileReader$BAMFileIterator.<init>(BAMFileReader.java:499)
at net.sf.samtools.BAMFileReader$BAMFileIterator.<init>(BAMFileReader.java:487)
at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:289)
at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:319)
at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:37)
at barna.io.sam.SAMReader$1.run(SAMReader.java:225)
at java.lang.Thread.run(Thread.java:662)