May I know the version of Adobe Reader you are using on iOS 9.1? Also please provide us more details of the workflow and/or function you are using with annotations.
We are currently working on the fix for the color problem with Text annotations.
The fix will be included in a future release of Acrobat Reader for iOS. (However, I am not able to speculate on a specific release date.)
We will let you know once the problem is fixed in Acrobat Reader. Thank you!
The latest version (15.2.0) of Acrobat Reader for iOS contains the fix for the text annotation color problem.
Would you please give it a try and let us know if it works for you now?