>>> '\u1ffc', '\u1ff3'
('ῼ', 'ῳ')
>>> '\u1ffc'.isupper()
False
>>> '\u1ff3'.islower()
True
>>> s = '\u1ff3\u1ff3\u1ffc\u1ffc'
>>> s
'ῳῳῼῼ'
>>> s.capitalize()
'ῼῳῼῼ'
>>>

lowering works
>>> '\u1ffc'
'ῼ'
>>> '\u1ffc'.lower()
'ῳ'
>>>

Indeed this seems a different issue, and might be worth fixing it.
Given this definition:
  str.capitalize()¶
      Return a copy of the string with its first character capitalized and the rest lowercased.
we might implement capitalize like:
>>> def mycapitalize(s):
...     return s[0].upper() + s[1:].lower()
... 
>>> 'fOoBaR'.capitalize()
'Foobar'
>>> mycapitalize('fOoBaR')
'Foobar'

And this would yield the correct result:
>>> s = u'\u1ff3\u1ff3\u1ffc\u1ffc'
>>> print s
ῳῳῼῼ
>>> print s.capitalize()
ῼῳῼῼ
>>> print mycapitalize(s)
ῼῳῳῳ
>>> s.capitalize().istitle()
False
>>> mycapitalize(s).istitle()
True

>>> import sys; hex(sys.maxunicode)
'0x10ffff'
>>> import unicodedata; unicodedata.unidata_version
'6.0.0'

>>> [len(x) for x in [Ll, Lu, Lt, Lo, Lm]]
[1759, 1436, 31, 97084, 210]
>>> sum(1 for c in Lu if c.lower() == c)
471  # uppercase chars with no lower
>>> sum(1 for c in Lt if c.lower() == c)
0    # titlecase chars with no lower
>>> sum(1 for c in Ll if c.upper() == c)
760  # lowercase chars with no upper
>>> sum(1 for c in Lo if c.upper() != c or c.title() != c or c.lower() != c)
0    # "Letter, other" chars with a different upper/title/lower case
>>> sum(1 for c in Lm if c.upper() != c or c.title() != c or c.lower() != c)
0    # "Letter, modifier" chars with a different upper/title/lower case
>>> sum(1 for c in all_chars if c not in L and (c.upper() != c or c.title() != c or c.lower() != c))
85   # non-letter chars with a different upper/title/lower case
>>> [c for c in all_chars if c not in L and (c.upper() != c or c.title() != c or c.lower() != c)]
['', 'Ⅰ', 'Ⅱ', 'Ⅲ', 'Ⅳ', 'Ⅴ', 'Ⅵ', 'Ⅶ', 'Ⅷ', 'Ⅸ', 'Ⅹ', 'Ⅺ', 'Ⅻ', 'Ⅼ', 'Ⅽ', 'Ⅾ', 'Ⅿ', 'ⅰ', 'ⅱ', 'ⅲ', 'ⅳ', 'ⅴ', 'ⅵ', 'ⅶ', 'ⅷ', 'ⅸ', 'ⅹ', 'ⅺ', 'ⅻ', 'ⅼ', 'ⅽ', 'ⅾ', 'ⅿ', 'Ⓐ', 'Ⓑ', 'Ⓒ', 'Ⓓ', 'Ⓔ', 'Ⓕ', 'Ⓖ', 'Ⓗ', 'Ⓘ', 'Ⓙ', 'Ⓚ', 'Ⓛ', 'Ⓜ', 'Ⓝ', 'Ⓞ', 'Ⓟ', 'Ⓠ', 'Ⓡ', 'Ⓢ', 'Ⓣ', 'Ⓤ', 'Ⓥ', 'Ⓦ', 'Ⓧ', 'Ⓨ', 'Ⓩ', 'ⓐ', 'ⓑ', 'ⓒ', 'ⓓ', 'ⓔ', 'ⓕ', 'ⓖ', 'ⓗ', 'ⓘ', 'ⓙ', 'ⓚ', 'ⓛ', 'ⓜ', 'ⓝ', 'ⓞ', 'ⓟ', 'ⓠ', 'ⓡ', 'ⓢ', 'ⓣ', 'ⓤ', 'ⓥ', 'ⓦ', 'ⓧ', 'ⓨ', 'ⓩ']
>>> list(c.lower() for c in _)
['', 'ⅰ', 'ⅱ', 'ⅲ', 'ⅳ', 'ⅴ', 'ⅵ', 'ⅶ', 'ⅷ', 'ⅸ', 'ⅹ', 'ⅺ', 'ⅻ', 'ⅼ', 'ⅽ', 'ⅾ', 'ⅿ', 'ⅰ', 'ⅱ', 'ⅲ', 'ⅳ', 'ⅴ', 'ⅵ', 'ⅶ', 'ⅷ', 'ⅸ', 'ⅹ', 'ⅺ', 'ⅻ', 'ⅼ', 'ⅽ', 'ⅾ', 'ⅿ', 'ⓐ', 'ⓑ', 'ⓒ', 'ⓓ', 'ⓔ', 'ⓕ', 'ⓖ', 'ⓗ', 'ⓘ', 'ⓙ', 'ⓚ', 'ⓛ', 'ⓜ', 'ⓝ', 'ⓞ', 'ⓟ', 'ⓠ', 'ⓡ', 'ⓢ', 'ⓣ', 'ⓤ', 'ⓥ', 'ⓦ', 'ⓧ', 'ⓨ', 'ⓩ', 'ⓐ', 'ⓑ', 'ⓒ', 'ⓓ', 'ⓔ', 'ⓕ', 'ⓖ', 'ⓗ', 'ⓘ', 'ⓙ', 'ⓚ', 'ⓛ', 'ⓜ', 'ⓝ', 'ⓞ', 'ⓟ', 'ⓠ', 'ⓡ', 'ⓢ', 'ⓣ', 'ⓤ', 'ⓥ', 'ⓦ', 'ⓧ', 'ⓨ', 'ⓩ']
>>> len(_)
85
>>> {unicodedata.category(c) for c in all_chars if c not in L and (c.upper() != c or c.title() != c or c.lower() != c)}
{'So', 'Mn', 'Nl'}