That's odd. Send the exe files from version 1.0 & 2.0 of your product & the wyBuild project file to wyatt@wyday.com.
Possible solution #1
If I were to guess at the problem I would say either the old EXE files or the new EXE files isn't being referenced correctly.
Open your wyBuild project, click the 1.0 version of your EXE file, note the "Local path". Now go to the 2.0 version and note the "Local path" of the same EXE files. Are the 2 paths different? They should be - they should reference the 2 versions of your app.
Possible solution #2
Did you Build wyUpdate for version 1.0 of your product? The version number of your product (what wyUpdate uses to download the correct patch files) is embedded in the "client.wyc" files. So you must be sure you included wyUpdate built for version 1.0 of your product.
You can rebuild wyUpdate for version 1.0 of your product by going to the Build page in wyBuild and selecting 1.0 from the drop-down. Then click "Build wyUpdate".
It's explained in the Video tutorial to wyBuild, AutomaticUpdater, and wyUpdate.