Below is the root cause of the problem.
In 10g, we get the file with ^M$(^M- Carriage return,$- Line feed) as delimiter for line.When the file goes to output folder it changes to $.
Whereas in 11g, the incoming file with ^M$ as delimiter remains as it is after getting moved to output folder.
So, ^M needs to be removed from file before moving to outbound folder.
In both 10g source FTP adapter has 'Read As Attachment' property set.
Also, target FTP adapter has File Type='ascii' with 'Put' operation.
We tried testing with same properties in 11g as well, but ^M was not removed.
Please help out in this regard.