Thanks for your reply.
Platform - PC
Application - 3B2 and Acrobat 9
So far we have seen this kind of issue in only one document. In the below screenshot you can see 2 pdf files, the right side one is my MS pdf and the left side one is the exported pdf from 3B2 application both the files having the special characters such as . I just did the text comparison however both and is missing in the exported pdf but the reports shown the changes for characters only wherever the charactes is missing the report not shown the changes properly(See highlighted in yellow).
Please let me know if you need more deatails.
There are no controls in the Compare Document feature which should be causing such a result, that I know of.
To report a bug (which this could be), it would have to be reproducable.
I'm a little confused about the application version you're on. In the title, you said Acrobat X. In your most recent reply, you said Acrobat 9.
If you can demonstrate a reproducable error in Acrobat X, it could be reported, so it could be fixed in Acrobat X or a later version.
It looks like when your 3B2 application is generating the PDF, the fonts aren't embedded. Then, when you open the file on you system, you're experiencing font substitution. To check this, look under File > Document Properties and check setting under the Font tab.
Also, when you compare the PDFs are you selecting "Reports" in the Document Description area of the Comparison Dialog?