In my experience, the difference in backup sizes is normal. I've found the software compression to be just as effective as hardware. My last full backup to disk was 699GB, but the duplicate to tape reports 359GB. That's a compression ratio of roughly 1.95:1 during the backup to disk. The duplicate to tape, however, can not compress the data any further, hence the reported 1.02:1 ratio on the tape. Unfortunately, Backup Exec will not report the compression ratio on a backup to disk device.
Hope this helps ease your fear! You could always do some test restore jobs as well.
-Scott