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In cases where Span Pro 1.4 has been used to generate TIFF/IT, and there is a problem where some of the transparent areas don't match the original Scitex page, it is almost certainly a problem with a preference setting in Span Pro.
The preference setting can be found by choosing the "Program Prefs..." option from the Preferences command in the Edit menu.
With the Program Prefs window opened, make sure that the "General Preferences" view is showing.
The preference that affects the transparent areas is "Disregard FLYT windows info".
For most users (perhaps all users) this option MUST be CHECKED. In case of doubts, they can try a problematic job both ways, but in our experience this option MUST be CHECKED.
Span Pro v1.5 (as of beta 2) has the same "Disregard FLYT windows" preference option, but in a slightly different place. In the Program Prefs window, it is now in the new "TIFF & TIFF/IT" view. But again, this option must be checked.
Both a final Page file and the LW contain transparency information, and in some cases it is identical. However, in some cases FAF (and possibly other operations) update the transparency information in the LW but not the page. Span Pro by default was designed to use the Page's information, but it is frequently out of synch, and it appears to be better to use the LW's transparency information.