Touch-up tool causes font issue in Acrobat 9 and X

While I edit text using the Edit Document Text tool (formerly TouchUp Text) the font style are getting changed, for example If i select the Uppercase style text using Document Text Tool after exit the selection and trying to save as  the doucment some characters with in the text changed into lower case. In Acrobat 7 and 8 the TouchUp Text tool works fine. Please suggest a solution to get rid of this issue in 9 pro and X pro.

Hi LoriAUC,
I have attached the screenshots  for your reference, How I selected the text and what the problem was occur in the pdf files. Actually this is pdf file which is exported from InDesign as per customer provided export settings. if I change 100% of subset fonts in that export settings(See the screenshots below) I can get rid of the font issues in Acrobat 9 and X pro but I am not supposed do any changes in that settings.
If you want check/analyze the problematic pdf file I can send it as an attachement to your mail ID? if so please let me know your mail ID.
Please let me know if you need any other details or questions to be clarified regrading this.
Thanks for your  support.

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