Can I show compliance using COMcheck if my glazing is over the 40% threshold in the 2009 IECC?

The Scope and Application sections of the 2009 IECC address use of ASHRAE 90.1 (2007) as an alternative.  See below for the text.  It is appropriate to use ASHRAE 90.1 as an alternative when your building exceeds 40% glazing, although it does not guarantee your building will comply.  ASHRAE offers an exception to the 40% limitation that calculates the partial shading provided by permanent opaque projections (Refer to ASHRAE 90.1-2007 Sections 5.5.4.2.1 and 5.5.4.4.1, Exception (b)).

 501.1 Scope.  The requirements contained in this chapter are applicable to commercial buildings, or portions of commercial buildings.  These commercial buildings shall meet either the requirements of ASHRAE/IESNA Standard 90.1, Energy Standard for Buildings Except for Low-Rise Residential Buildings, or the requirements contained in this chapter.

 501.2 Application.  The commercial building project shall comply with the requirements in Sections 502 (Building envelope requirements), 503 (Building mechanical systems), 504 (Service water heating) and 505 (Electrical power and lighting systems) in its entirety.  As an alternative the commercial building project shall comply with the requirements of ASHRAE/IESNA 90.1 in its entirety.  Exception:  Buildings conforming to Section 506, provided sections 502.4, 503.2, 504, 505.2, 505.3, 505.4, 505.6 and 505.7 are each satisfied.