cuffcompare: transcripts without strand and output combined

[alexnico84]

I have two questions about cuffcompare:

1) When I compare two annotation cuffcompare it does not find overlap between transcripts without strand (eg. with dot). Why?
2) When using cuffcompare for combining multiple gtf, the combined file output changes according to the order of the input files which is passed to cuffcompare.
For example:
cuffcompare a1.gtf a2.gtf a3.gtf
cuffcompare a2.gtf a1.gtf a3.gtf
will produce slightly different results in the output stdout.combined.gtf

I would really appreciate some explanations.
Thanks
Nicola