On Skritter, meanings are solely attached to the writing of a character, not to the pronunciation. In some cases, this lack of differentiation makes learning definitions and tones both difficult and confusing.
For instance, when you study 宁愿 the meaning that is shown for 宁 is the same as when you study 宁静. However, in 宁静the 宁 is second tone and means "peaceful", in 宁可 it's fourth tone and means "preferably". On Skritter, it always says "peaceful; tranquil; serene, rather; prefer; Ningxia autonomous region (abbr.)".
Note that in the definition given above there's a comma between "serene" and "rather" (note the standard semicolon), so I guess you've merged two separate database entries.
I'm not sure about whether or not it's easy to implement, but including the different tones or, alternatively, only showing the appropriate definition would be a great feature and save me a lot of time (finally reduce the study intervals for the tones of these annoying characters).
Other common examples:
相: http://www.google.com/dictionary?langpair=zh-CN|en&q=相
尽: http://www.google.com/dictionary?langpair=zh-CN|en&q=尽
差: http://www.google.com/dictionary?langpair=zh-CN|en&q=差
为: http://www.google.com/dictionary?langpair=zh-CN|en&q=为
阿: http://www.google.com/dictionary?langpair=zh-CN|en&q=阿
(One of those characters where there's even more than just a tone change, can also be pronounced "e1"="flatter")
see also: http://www.skritter.com/forum/topic?id=38919409
-- 穆儿