1) Are elements in File2.gff overlapping? If so, you might have an issue where intervals are merged beforehand.
If all of an element in File1.bed is contained inside a merged interval from File2.gff, it is possible that the File1.bed element would not be contained entirely inside the intervals from File2.gff that make up that merge.
Consider the following cartoons. Here's element A:
A: <-----------[ ]----------->
Now consider two elements from B, B1 and B2, which can be merged internally into something like B* for set operations:
B1: <---------[ ]------------->
B2: <------------[ ]---------->
B*: <---------[ ]---------->
A is contained entirely within B* and would get misreported, even though it is not contained entirely within B1 or B2.
Maybe try a different toolkit:
$ sort-bed File1.bed > File1.sorted.bed
$ gff2bed < File2.gff > File2.sorted.bed
$ bedmap --echo --fraction-ref 1 File1.sorted.bed File2.sorted.bed > Out.file
This reports (--echo) elements in File1.sorted.bed which are contained entirely (--fraction-ref 1) within elements in File2.sorted.bed.
2) Are contig/chromosome names or name schemes identical in File1.bed and File2.gff? If you have an interval with Chr1 in one file, and an interval with chr1 in another, set operations between the two will treat those as intervals from different chromosomes.
