There shouldn't have been any custom GUIDs used, I used only the following which are all default:
D2E16D2B-692A-4BFC-8383-B1A1A815A3E8 - Shorelines Generic Bay Harbor
7B3229D8-18ED-4F4D-AE22-12660862ABA1 - Shorelines Generic Lake
E5DD8B66-8E86-4E7E-BE58-6E94A91C8FF0 - Hydro_Generic_River_Perennial
BCD5C182-9C8B-4C57-97BD-272CF492CBFF - Hydro_Generic_Lake_Perennial
0CBC8FAD-DF73-40A1-AD2B-FE62F8004F6F - Exclude_All_Shorelines
956A42AD-EC8A-41BE-B7CB-C68B5FF1727E - Exclude_All_Water_Polygons
Here's the .sbp file for SBuilder:
http://www.cat-tamer.com/flightsim/atchmnts/qmid_1137_128.SBP.zip
Note: The .spb file contains no excludes, I usually don't save them with the excludes in place because then the exclusion polys get in the way when you're trying to finish up the hydro polys and shorelines. Also in the .zip though is qmid_1137_128_excludes.SBX which contains the excludes in a separate file. The idea is you work on your hydro polys and shorelines and whenever you're ready to export a .bgl you save the project (the .spb) and then do file > append > Sbuilder SBX, appending qmid_1137_128_excludes.SBX. After appending the excludes select > all lines and select > all polygons then export a .bgl and close without saving the excludes into the file.
I'll take a look at your shapes.
EDIT: I can't see anything wrong with your .shps, here's a .bgl I compiled and tried on my own system with default CVX, it seems to work the same as mine (except your shorelines have a lot more detail than mine, lol):
http://www.cat-tamer.com/flightsim/atchmnts/CVX_Rustams_shapes.zip
Jim