Look like we are able to fix it, just got into more details and found in program/steps/utils/save_pref.inc
line 18 has following code <$Id: save_pref.inc 4410 2011-01-12 18:25:02Z thomasb $> whereas patch file was looking for <$Id$>.
Since patch file is removing this line, I thought of replacing original code with expected code from patch file and it worked well.
I hope this should work well.
I have one old live server with 5.3 version, one quick question - will 6.x patch work on roundcube 5.3 version
thanks in advance.
Regards,
PineMailAdmin