There are 4 different output formats. All of them contain at top the names of the compared files. But you are right, there is a problem with comparing PDF files as UC must extract the text within the PDF files to temporary files. On comparison of PDF files the output file contains the names of the temporary files instead of the PDF files. The name of temporary files are of no use for anybody. I will report this special issue to IDM support by email.
You can workaround this issue with following commands in your batch file:
echo [ 1 ] D:\Test1\Smile1.pdf>D:\Test\output1.txt
echo [ 2 ] D:\Test2\Smile2.pdf>>D:\Test\output1.txt
uc -t "D:\Test1\Smile1.pdf" "D:\Test2\Smile2.pdf" -ne -op "D:\Test\output1.txt"
echo [ 1 ] D:\Test1\Smile3.pdf>D:\Test\output2.txt
echo [ 2 ] D:\Test2\Smile4.pdf>>D:\Test\output2.txt
uc -t "D:\Test1\Smile3.pdf" "D:\Test2\Smile4.pdf" -ne -op "D:\Test\output2.txt"
The echo commands write 2 lines at top of the 2 output files with the names of the PDF files compared and UC appends the output of the comparisons.