Just a SWAG, but are all the file names UNIQUE if zipping multiple folders? If not, are you using recursion so the path is saved with the filename? If not, then the last file of the same name is what gets zipped. The following are what I usually have set in my DynaZip class for zipping files:

cZip_ItemList = "c:\myfiles\*.*"
lZip_Recurse = .T.      && Directory is traveled recursively
lZip_NoDirNames = .F.   && Store path names for ZIP file items if TRUE
lZip_AfterDate = .F.    && Include only items on or after the data in dZip_TheDate
dZip_TheDate = {}       && Only used if lZip_AfterDate is TRUE.
lZip_IncFlag = .F.      && Items that match specs in cZip_IncList are 
                        ** INCLUDED in the operation
cZip_IncList = ""       && Separate each filespec with a space.
                        ** Place "Quotes" around long filenames.
                        ** Only used if lZip_IncFlag is TRUE
lZip_ExcFlag = .F.      && Items that match specs in cZip_ExcList are
                        ** EXCLUDED from the operation
cZip_ExcList = ""       && Separate each filespec with a space.
                        ** Place "Quotes" around long filenames.
                        ** Only used if lZip_ExcFlag is TRUE
lZip_NoDirEntries = .T. && If FALSE, directories ARE added as items
                        ** to the ZIP file except when lZip_NoDirNames
                        ** is TRUE. If both are FALSE, and the item list
                        ** includes C:\ABC\D.PCX, then 2 items
                        ** are added to the ZIP file -- ABC/
                        ** [a directory] and ABC/D.PCX [ a file]

lZSO_SkipLockedFiles = .F.  && Skip files that are currently in exclusive
                            ** use or locked by some other process.
lZSO_Just_Archived = .F.    && Only zip files whose Archive bit is set.
lZSO_Reset_Archived = .F.   && Turn off the Archive bit for each file that
                            ** is successfully zipped. Only used if
                            ** lZSO_Just_Archived is TRUE