The simple glazing model works by taking a very basic description of the glazing system, then the surface (film) coefficients are stripped off and a match is made with some standard glazing system types, the parameters of these are adjusted through interpolation between the standard systems and then the film coefficients are added at simulation time. The U-value and other properties reported in the eio file may use slightly different film coefficients to those assumed in the input and this can give rise to small differences between input and output. This does not reflect on the overall accuracy of the simulations though.

Also, this response from Brent Griffith from EnergyPlus support:

"This issue held up release of the simple window model for 6 months.  I have checked and recheck it many times and in the end decided, after much review, to release it without exact agreement between input and the eio reporting, because the modelling just doesn't work that way and exact agreement is not expected."