I'd like to second this request from September 2013 for the Guitar Window to support non-standard tunings:
http://www.pgmusic.com/forums/ubbthreads.php?ubb=showflat&Number=214113#Post214113

In my case, I would set it to "All Fourths" tuning (EADGCF), where just the 2 high strings are tuned 1/2 step higher:
http://en.wikipedia.org/wiki/All_fourths_tuning

By the way, there are some great players using alternate tunings, such as Stanley Jordan and Alex Hutchings (both use All Fourths). There is a growing Facebook "Guitar Tuning in 4ths" group:
https://www.facebook.com/groups/183968224067/

Some Android and iOS chord/scale reference apps support non-standard tunings very nicely, and they are a great development, but such support in BIAB would be much more valuable.
https://play.google.com/store/apps/details?id=com.rabugentom.chordfree

A BIAB Guitar Window supporting custom tunings would be a great learning tool.