Cuffcompare merged.gtf to self not all "="

[travis_jensen123]

I have been working on comparing the results of 20 merged.gtf files to see the differences between each pair of files. When doing this work, I used the following type of command:
cuffcompare -p 4 -r merged_1.gtf -o ./compare/merged2_vs_1 merged_2.gtf

This should use merged_1.gtf as the "reference" and compare merged_2.gtf to it. However, I noticed that if merged_1.gtf and merged_2.gtf are switched the results are different. Furthermore, if I compare merged_1.gtf to itself ( merged_1.gtf), not all of the class codes are "=". I actually get something like this:

"Class_code" #_occurrences_in_.tmap_file
"=" 215622
"u" 11040
"p" 1172
"c" 1051
"i" 1707

How can this be the case? if I compare something to itself, I should expect all class codes to be "=".

Any thoughts?