Hi Indaarjit,
A few points to troubleshoot the issue -
1. By referring screenshot you had shared, Baseline version screenshot shows data from Year 2016 buckets whereas Version1 shows data from Year 2014 buckets. Please make sure this is not the reason for this mismatch.
2. When you execute Copy Version operator in Excel, please double check the filter settings - both Attribute and TIME, and keyfigure selected for copy.
3. As you are using Version Specific Master Data, it is important both Source and Target versions has same master data in them. It seems this is being taken care by you as I see the MDT having same values for both versions.
4. It is good idea to display data from both version together. In Edit View - try selecting both versions at the same time to display their data. This will make comparison much easier.
Hope this will help.
Thank you
Satish Waghmare