Hi,
try the following:
1. Make a backup of your "cfg" folder in case you've already customized your JD settings.
2. Delete/uninstall your current JD.
3. Install the 64bit version from here:
https://jdownloader.org/jdownloader2
4. If needed, copy over your old .cfg folder.
-psp-
EDIT
Our 32bit launcher cannot start a 64bit JVM which is why the .jar without launcher will work.
The exe needs a 32bit dll thus you should re-install the 64bit version.