Please, let me know the followings:
-which version of JChem for Excel are you using: 15.4.13?
-what is you MS Office version: Office 2010, 64bit in Windows7?
Did you convert the SMILES string exactly the same way as previously?
Please, check if the option in JChem for Excel: CD Clean During String Conversion is set to True, and what is the status of the option: "Structure Display/Preferences-Bonds/Aromatic Bonds as Discrete Double Bonds"
As far as I see from the screenshots, the first 2 structures have 3D coordinates, the second have only 2D.
The hydrogens should be saved in the sdfile when exporting, but depending on the display options, they are not visible. Please try the following:
1. double-click on the structure: Marvin editor opens.
2. In Marvin, in Structure menu, press Add/Explicit Hydrogens: now all the hydrogens should be displayed in Marvin.
3. Press Ctrl+A, then Ctrl+C, close Marvin editor.
4. Go to an Excel cell and press Ctrl+V. Please, check if the hydrogens are now all visible.
Hope this helps, but let me know, if you have further questions.