merging with Legacy

I am a dedicated Legacy user and after extensive use, this is my first problem. I have been maintaining two trees, one on my computer and one on ancestry.com, both quite large. I recently downloaded the ancestry tree and am attempting to merge it with my computer-based file. however, the merge is causing me a gross amount of unnecessary tedious work because it does not recognize duplicates even when the spelling is identical, the parents are identical, and the spouse is identical. In 99% of the cases, the only difference is the user ID; and that is totally unimportant (to me). I have looked and looked and cannot find a place to turn off that comparison. I did find one, but it is already unchecked.
Any recommendations?