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In Python 2, PyErr_GivenExceptionMatches [1] calls PyObject_IsSubclass. To handle calling __subclasscheck__ in this case, 2.7 (but not 2.6) temporarily increases the recursion limit by 5. For example:
 class CMeta(type):
 def __subclasscheck__(self, other):
 import sys
 print 'recursion limit: %d' % sys.getrecursionlimit()
 frame = sys._getframe(1)
 n = 0
 while frame:
 n += 1
 frame = frame.f_back
 print 'frame: %d' % n
 return True
 class C(Exception):
 __metaclass__ = CMeta
 def f():
 try:
 f()
 except C:
 pass
 >>> sys.getrecursionlimit()
 1000
 >>> f()
 recursion limit: 1005
 frame: 1000
 >>> sys.getrecursionlimit()
 1000
If the recursion limit weren't temporarily increased, then trying to call __subclasscheck__ in the above case would raise another RuntimeError.
In Python 3, PyErr_GivenExceptionMatches [2] instead calls PyType_IsSubtype. See issue 2534. In that issue Antoine's reason for the change is that "otherwise there are some nasty issues with recursion checking". 
[1]: https://hg.python.org/cpython/file/v2.7.10/Python/errors.c#l84
[2]: https://hg.python.org/cpython/file/v3.5.0/Python/errors.c#l166