When you load an existing project and the takeoff does not line up, it's most likely due to  the User Preference for "Extract bitmaps from PDF files containing a single bitmap" is most likely different than what it was set to originally.

To resolve the issue, click on Admin/User Preferences (Classic Toolbar) or Settings/ User Preferences (Ribbon Bar). Click on the Files tab and either check or uncheck the preference "Extract bitmaps from PDF files containing a single bitmap".

Please see the eTakeoff HELP below for an explanation on the "Extract bitmaps from PDF files". 

Drawings are frequently provided as PDF files containing a scanned image of the drawing (a bitmap). Extracting the bitmap allows it to be loaded, displayed and zoomed much more rapidly. Check this option to use bitmap extraction. If this option is checked, PDF files containing a single bitmap will NOT be automatically converted to TIFF files because there is no performance advantage.

WARNING: The extracted bitmaps may have a different resolution than the original PDF file. That means that any measurements made on the original PDF file may need to be re-done. If the original bitmaps were converted to TIFF files, there will be no problem.

This option will be checked on all new installations and it will be disabled so that it can't be un-checked. This avoids the resolution problem described above. If you need to un-check this option, click on one of the other tabs of the preferences window. Then hold the Shift key down while clicking on the "Conversion" tab. The option will be enabled.